diff --git a/docs/middleware.md b/docs/middleware.md
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--- /dev/null
+++ b/docs/middleware.md
@@ -0,0 +1,34 @@
+# Middleware Management API 
+
+## Overview
+
+The Middleware Management API provides REST endpoints for dynamically managing middleware components in proTES at runtime. This API allows administrators and developers to add, configure, update, and remove middleware without service restarts.
+
+## Background
+
+proTES uses a middleware architecture to process task execution requests. Previously, middleware configuration was static and required service restarts for any changes. The Middleware Management API enables dynamic runtime configuration, making it easier to adapt the service to changing requirements and deploy new middleware components.
+
+## API Specification
+
+The Middleware Management API is defined using OpenAPI 3.0 specification. For comprehensive, interactive documentation with the ability to explore endpoints, request/response schemas, and examples, please visit:
+
+**[Swagger Editor - Middleware Management API](https://editor.swagger.io/?url=https://raw.githubusercontent.com/elixir-cloud-aai/proTES/refs/heads/dev/pro_tes/api/middleware_management.yaml)**
+
+The interactive documentation provides:
+- Complete endpoint definitions with request/response examples
+- Detailed schema specifications for all data models
+- Parameter descriptions and validation rules
+- Error response definitions
+- The ability to test API calls directly
+
+## File Structure
+
+```
+pro_tes/
+├── api/
+│   └── middleware_management.yaml          (OpenAPI specification)
+└── config.yaml                             (References the specification)
+
+docs/
+└── middleware.md                           (This documentation)
+```
\ No newline at end of file
diff --git a/pro_tes/api/middleware_management.yaml b/pro_tes/api/middleware_management.yaml
new file mode 100644
index 0000000..add9fd7
--- /dev/null
+++ b/pro_tes/api/middleware_management.yaml
@@ -0,0 +1,685 @@
+openapi: 3.0.3
+info:
+  title: proTES Middleware Management API
+  description: |
+    API for dynamically managing middleware in proTES (GA4GH Task Execution Service Proxy).
+    This API allows runtime configuration of middleware components that process task execution requests.
+  version: 1.0.0
+  contact:
+    name: ELIXIR Cloud & AAI
+    url: https://github.com/elixir-cloud-aai/proTES
+  license:
+    name: Apache 2.0
+    url: https://www.apache.org/licenses/LICENSE-2.0.html
+
+servers:
+  - url: /protes/v1
+    description: proTES Middleware Management API base path
+
+tags:
+  - name: Middleware Management
+    description: Operations for managing middleware stack
+
+paths:
+  /middlewares:
+    get:
+      summary: List all middlewares
+      description: |
+        Retrieve all configured middlewares with their order and metadata.
+        Results are sorted by execution order (ascending) by default.
+      operationId: ListMiddlewares
+      tags:
+        - Middleware Management
+      parameters:
+        - name: page_size
+          in: query
+          description: Maximum number of results to return per page
+          required: false
+          schema:
+            type: integer
+            minimum: 1
+            maximum: 100
+            default: 50
+        - name: page
+          in: query
+          description: Page number to retrieve (0-indexed)
+          required: false
+          schema:
+            type: integer
+            minimum: 0
+            default: 0
+        - name: sort_by
+          in: query
+          description: Field to sort by
+          required: false
+          schema:
+            type: string
+            enum: [order, name, created_at, updated_at]
+            default: order
+        - name: sort_order
+          in: query
+          description: Sort order direction
+          required: false
+          schema:
+            type: string
+            enum: [asc, desc]
+            default: asc
+        - name: source
+          in: query
+          description: Filter by middleware source type
+          required: false
+          schema:
+            type: string
+            enum: [local, git, pypi]
+      responses:
+        '200':
+          description: Successful response with list of middlewares
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/MiddlewareList'
+        '400':
+          description: Bad request (invalid parameters)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '401':
+          description: Unauthorized (when authentication is configured)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '403':
+          description: Forbidden (when authentication is configured and permissions are insufficient)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '500':
+          description: Internal server error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+
+    post:
+      summary: Add a new middleware
+      description: |
+        Add a new middleware to the execution stack. Middleware can be loaded from:
+        - Git repositories: Git repositories containing setup.py or pyproject.toml (recommended)
+        - PyPI packages: Packages from PyPI or other package registries (recommended)
+        - Local packages: Installed Python packages or local file paths (**deprecated** - for development only)
+        
+        The middleware will be appended to the end of the execution stack. To change the execution 
+        order, use the PUT /middlewares/reorder endpoint after creation.
+        
+        If name is not provided, it will be derived from the package or repository name.
+        
+        Fallback groups can be created by providing an array of source configurations.
+        If the first middleware in the group fails, the system tries the next one in the 
+        fallback group, allowing mixed sources (Git, PyPI, local) in a single entry.
+        
+        **Note:** Fallback groups are managed as atomic units. To modify the middlewares 
+        within a fallback group (add/remove/reorder sources), you must delete and recreate 
+        the entire fallback group. Individual middlewares within a group cannot be modified 
+        separately due to security constraints on source configuration changes.
+      operationId: AddMiddleware
+      tags:
+        - Middleware Management
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/Middleware'
+            examples:
+              git_middleware:
+                summary: Add middleware from Git repository
+                value:
+                  name: "Custom Load Balancer"
+                  source:
+                    type: "git"
+                    package_location: "https://github.com/user/repo.git"
+                    entry_point: "custom_middleware.LoadBalancer"
+              pypi_middleware:
+                summary: Add middleware from PyPI
+                value:
+                  name: "Third-party Middleware"
+                  source:
+                    type: "pypi"
+                    package_location: "protes-middleware-custom"
+                    entry_point: "custom.Middleware"
+                    version: "1.0.0"
+              local_middleware:
+                summary: Add local middleware (deprecated - development only)
+                value:
+                  name: "Distance-based Router"
+                  source:
+                    type: "local"
+                    entry_point: "pro_tes.plugins.middlewares.task_distribution.distance.TaskDistributionDistance"
+              local_middleware_with_path:
+                summary: Add local middleware with file path
+                value:
+                  name: "Custom Local Middleware"
+                  source:
+                    type: "local"
+                    package_location: "/opt/middleware/custom"
+                    entry_point: "custom.Middleware"
+              fallback_group:
+                summary: Add fallback group with mixed sources
+                value:
+                  name: "Load Balancing Group"
+                  source:
+                    - type: "git"
+                      package_location: "https://github.com/org/primary.git"
+                      entry_point: "primary.DistanceRouter"
+                    - type: "git"
+                      package_location: "https://github.com/org/fallback.git"
+                      entry_point: "fallback.RandomRouter"
+                    - type: "pypi"
+                      package_location: "protes-fallback"
+                      entry_point: "fallback.LastResort"
+      responses:
+        '201':
+          description: Middleware created successfully
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/MiddlewareCreateResponse'
+        '400':
+          description: Invalid request (duplicate name/entry_point, invalid source, validation failed)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '401':
+          description: Unauthorized (when authentication is configured)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '403':
+          description: Forbidden (when authentication is configured and permissions are insufficient)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '500':
+          description: Internal server error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+
+  /middlewares/{middleware_id}:
+    get:
+      summary: Get middleware details
+      description: Retrieve detailed information about a specific middleware by ID
+      operationId: GetMiddleware
+      tags:
+        - Middleware Management
+      parameters:
+        - name: middleware_id
+          in: path
+          description: Unique identifier of the middleware
+          required: true
+          schema:
+            type: string
+            pattern: '^[a-f0-9]{24}$'
+      responses:
+        '200':
+          description: Successful response with middleware details
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Middleware'
+        '400':
+          description: Bad request (invalid middleware ID format)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '401':
+          description: Unauthorized (when authentication is configured)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '403':
+          description: Forbidden (when authentication is configured and permissions are insufficient)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '404':
+          description: Middleware not found
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '500':
+          description: Internal server error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+
+    patch:
+      summary: Update middleware configuration
+      description: |
+        Partially update middleware configuration. Only name and config fields
+        can be updated. Source configuration and execution order cannot be modified.
+        Use PUT /middlewares/reorder to change execution order.
+      operationId: UpdateMiddleware
+      tags:
+        - Middleware Management
+      parameters:
+        - name: middleware_id
+          in: path
+          description: Unique identifier of the middleware
+          required: true
+          schema:
+            type: string
+            pattern: '^[a-f0-9]{24}$'
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/MiddlewareUpdate'
+      responses:
+        '200':
+          description: Middleware updated successfully
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Middleware'
+        '400':
+          description: Invalid request (invalid middleware ID format, invalid parameters)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '401':
+          description: Unauthorized (when authentication is configured)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '403':
+          description: Forbidden (when authentication is configured and permissions are insufficient)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '404':
+          description: Middleware not found
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '409':
+          description: Conflict (e.g., duplicate name)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '500':
+          description: Internal server error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+
+    delete:
+      summary: Remove a middleware
+      description: |
+        Permanently remove a middleware from the execution stack and database.
+        This operation works for both individual middlewares and fallback groups (which are 
+        removed as a single unit).
+      operationId: DeleteMiddleware
+      tags:
+        - Middleware Management
+      parameters:
+        - name: middleware_id
+          in: path
+          description: Unique identifier of the middleware
+          required: true
+          schema:
+            type: string
+            pattern: '^[a-f0-9]{24}$'
+      responses:
+        '204':
+          description: Middleware deleted successfully
+        '400':
+          description: Bad request (invalid middleware ID format)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '401':
+          description: Unauthorized (when authentication is configured)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '403':
+          description: Forbidden (when authentication is configured and permissions are insufficient)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '404':
+          description: Middleware not found
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '500':
+          description: Internal server error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+
+  /middlewares/reorder:
+    put:
+      summary: Reorder middleware stack
+      description: |
+        Reorder the entire middleware execution stack by providing an ordered array
+        of middleware IDs. All middleware IDs must be provided in the desired execution order.
+      operationId: ReorderMiddlewares
+      tags:
+        - Middleware Management
+      requestBody:
+        required: true
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/MiddlewareOrder'
+      responses:
+        '200':
+          description: Middlewares reordered successfully
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  message:
+                    type: string
+                    example: "Middleware stack reordered successfully"
+                  middlewares:
+                    type: array
+                    items:
+                      $ref: '#/components/schemas/Middleware'
+        '400':
+          description: Invalid request (missing IDs, invalid IDs, duplicate IDs)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '401':
+          description: Unauthorized (when authentication is configured)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '403':
+          description: Forbidden (when authentication is configured and permissions are insufficient)
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+        '500':
+          description: Internal server error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorResponse'
+
+components:
+  schemas:
+    Middleware:
+      type: object
+      description: Middleware configuration object used for both requests and responses
+      required:
+        - source
+      properties:
+        id:
+          type: string
+          description: Unique identifier
+          readOnly: true
+          example: "507f1f77bcf86cd799439011"
+        name:
+          type: string
+          description: Human-readable name for the middleware. If not provided, derived from package or repository name.
+          nullable: true
+          minLength: 1
+          maxLength: 255
+          example: "Distance-based Router"
+        source:
+          oneOf:
+            - $ref: '#/components/schemas/MiddlewareSource'
+            - type: array
+              description: Fallback group (array of middleware sources)
+              items:
+                $ref: '#/components/schemas/MiddlewareSource'
+              minItems: 2
+              example:
+                - type: "git"
+                  package_location: "https://github.com/org/primary.git"
+                  entry_point: "primary.DistanceRouter"
+                - type: "git"
+                  package_location: "https://github.com/org/fallback.git"
+                  entry_point: "fallback.RandomRouter"
+        order:
+          type: integer
+          description: Execution order (0 = first). Assigned by system on creation or via /middlewares/reorder endpoint.
+          minimum: 0
+          readOnly: true
+          example: 0
+        config:
+          type: object
+          description: Middleware-specific configuration
+          nullable: true
+          additionalProperties: true
+          example:
+            timeout: 30
+            retries: 3
+        created_at:
+          type: string
+          format: date-time
+          description: Creation timestamp (set by system)
+          readOnly: true
+          example: "2026-01-24T10:30:00Z"
+        updated_at:
+          type: string
+          format: date-time
+          description: Last update timestamp (set by system)
+          readOnly: true
+          example: "2026-01-24T10:30:00Z"
+
+    MiddlewareSource:
+      type: object
+      description: Middleware package source configuration
+      required:
+        - type
+        - entry_point
+      properties:
+        type:
+          type: string
+          description: Source type for the middleware package
+          enum: [local, git, pypi]
+        entry_point:
+          type: string
+          description: Class path entry point (e.g., 'package.module.ClassName')
+          example: "pro_tes.plugins.middlewares.task_distribution.distance.TaskDistributionDistance"
+        version:
+          type: string
+          description: Package version (optional, for pypi or git tag/branch)
+          example: "1.0.0"
+        package_location:
+          type: string
+          description: The location of the package (format and requirement vary by type).
+      discriminator:
+        propertyName: type
+        mapping:
+          local: '#/components/schemas/MiddlewareLocal'
+          git: '#/components/schemas/MiddlewareGit'
+          pypi: '#/components/schemas/MiddlewarePyPi'
+      oneOf:
+        - $ref: '#/components/schemas/MiddlewareLocal'
+        - $ref: '#/components/schemas/MiddlewareGit'
+        - $ref: '#/components/schemas/MiddlewarePyPi'
+
+    MiddlewareLocal:
+      allOf:
+        - $ref: '#/components/schemas/MiddlewareSource'
+        - type: object
+          properties:
+            package_location:
+              type: string
+              description: >
+                Local file path to directory containing package. 
+                Optional if the package is already installed in the environment.
+              pattern: '^/.*'
+              example: "/path/to/my/middleware/package"
+
+    MiddlewareGit:
+      allOf:
+        - $ref: '#/components/schemas/MiddlewareSource'
+        - type: object
+          required:
+            - package_location
+          properties:
+            package_location:
+              type: string
+              format: uri
+              description: Git repository URL (must end in .git).
+              pattern: '^https://github\.com/.+\.git$'
+              example: "https://github.com/user/repo.git"
+
+    MiddlewarePyPi:
+      allOf:
+        - $ref: '#/components/schemas/MiddlewareSource'
+        - type: object
+          required:
+            - package_location
+          properties:
+            package_location:
+              type: string
+              description: The registered name of the package on PyPi.
+              pattern: '^[a-zA-Z0-9\-_.]+$'
+              example: "protes-middleware-custom"
+
+    MiddlewareUpdate:
+      type: object
+      description: Request body for updating a middleware (partial update)
+      properties:
+        name:
+          type: string
+          description: Human-readable name for the middleware
+          minLength: 1
+          maxLength: 255
+          example: "Distance-based Router v2"
+        config:
+          type: object
+          description: Middleware-specific configuration
+          nullable: true
+          additionalProperties: true
+          example:
+            timeout: 60
+            retries: 5
+
+    MiddlewareList:
+      type: object
+      description: Paginated list of middlewares
+      required:
+        - middlewares
+        - pagination
+      properties:
+        middlewares:
+          type: array
+          description: Array of middleware configurations
+          items:
+            $ref: '#/components/schemas/Middleware'
+        pagination:
+          type: object
+          description: Pagination information following GA4GH guidelines
+          required:
+            - page
+            - page_size
+            - total
+          properties:
+            page:
+              type: integer
+              description: Current page number (0-indexed)
+              example: 0
+            page_size:
+              type: integer
+              description: Number of results per page
+              example: 50
+            total:
+              type: integer
+              description: Total number of middlewares available
+              example: 5
+            total_pages:
+              type: integer
+              description: Total number of pages available
+              example: 1
+
+    MiddlewareCreateResponse:
+      type: object
+      description: Response after creating a middleware
+      required:
+        - id
+        - order
+        - message
+      properties:
+        id:
+          type: string
+          description: Unique identifier of created middleware
+          example: "507f1f77bcf86cd799439011"
+        order:
+          type: integer
+          description: Assigned execution order
+          example: 0
+        message:
+          type: string
+          description: Success message
+          example: "Middleware added successfully"
+
+    MiddlewareOrder:
+      type: object
+      description: Request body for reordering middlewares
+      required:
+        - ordered_ids
+      properties:
+        ordered_ids:
+          type: array
+          description: Array of middleware IDs in desired execution order
+          items:
+            type: string
+            pattern: '^[a-f0-9]{24}$'
+          minItems: 1
+          example:
+            - "507f1f77bcf86cd799439011"
+            - "507f1f77bcf86cd799439012"
+            - "507f1f77bcf86cd799439013"
+
+    ErrorResponse:
+      type: object
+      description: Standard error response
+      required:
+        - code
+        - message
+      properties:
+        code:
+          type: integer
+          description: HTTP status code
+          example: 404
+        message:
+          type: string
+          description: Human-readable error message
+          example: "Middleware with ID '507f1f77bcf86cd799439011' not found"
\ No newline at end of file
diff --git a/pro_tes/config.yaml b/pro_tes/config.yaml
index 609900c..cbacef1 100644
--- a/pro_tes/config.yaml
+++ b/pro_tes/config.yaml
@@ -47,6 +47,16 @@ db:
           indexes:
             - keys:
                 id: 1
+        middlewares:
+          indexes:
+            - keys:
+                name: 1
+              options:
+                "unique": True
+            - keys:
+                class_path: 1
+              options:
+                "unique": True
 
 # API configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.APIConfig
@@ -71,6 +81,16 @@ api:
         options:
           swagger_ui: True
           serve_spec: True
+    - path:
+        - api/middleware_management.yaml
+      add_operation_fields:
+        x-openapi-router-controller: pro_tes.api.middlewares.controllers
+      connexion:
+        strict_validation: True
+        validate_responses: True
+        options:
+          swagger_ui: True
+          serve_spec: True
 
 # Logging configuration
 # Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.LogConfig