Dependabot Configuration & Management

Overview

Dependabot is GitHub's built-in dependency management tool with three core capabilities:

1. Dependabot Alerts — Notify when dependencies have known vulnerabilities (CVEs)
2. Dependabot Security Updates — Auto-create PRs to fix vulnerable dependencies
3. Dependabot Version Updates — Auto-create PRs to keep dependencies current

All configuration lives in a single file: .github/dependabot.yml on the default branch. GitHub does not support multiple dependabot.yml files per repository.

Configuration Workflow

Follow this process when creating or optimizing a dependabot.yml:

Step 1: Detect All Ecosystems

Scan the repository for dependency manifests. Look for:

Notes:

• pnpm and yarn both use the npm ecosystem value.
• Prefer uv ecosystem value when uv.lock is present; otherwise use pip.

Step 2: Map Directory Locations

For each ecosystem, identify where manifests live. Use directories (plural) with glob patterns for monorepos:

directories:
  - "/"           # root
  - "/apps/*"     # all app subdirs
  - "/packages/*" # all package subdirs
  - "/lib-*"      # dirs starting with lib-
  - "**/*"        # recursive (all subdirs)

Important: directory (singular) does NOT support globs. Use directories (plural) for wildcards.

Step 3: Configure Each Ecosystem Entry

Every entry needs at minimum:

- package-ecosystem: "npm"
  directory: "/"
  schedule:
    interval: "weekly"

Step 4: Optimize with Grouping, Labels, and Scheduling

See sections below for each optimization technique.

Monorepo Strategies

Glob Patterns for Workspace Coverage

For monorepos with many packages, use glob patterns to avoid listing each directory:

- package-ecosystem: "npm"
  directories:
    - "/"
    - "/apps/*"
    - "/packages/*"
    - "/services/*"
  schedule:
    interval: "weekly"

Cross-Directory Grouping

Use group-by: dependency-name to create a single PR when the same dependency updates across multiple directories:

groups:
  monorepo-deps:
    group-by: dependency-name

This creates one PR per dependency across all specified directories, reducing CI costs and review burden.

Limitations:

• All directories must use the same package ecosystem
• Applies to version updates only
• Incompatible version constraints create separate PRs

Standalone Packages Outside Workspaces

If a directory has its own lockfile and is NOT part of the workspace (e.g., scripts in .github/), create a separate ecosystem entry for it.

Dependency Grouping

Reduce PR noise by grouping related dependencies into single PRs.

By Dependency Type

groups:
  dev-dependencies:
    dependency-type: "development"
    update-types: ["minor", "patch"]
  production-dependencies:
    dependency-type: "production"
    update-types: ["minor", "patch"]

By Name Pattern

groups:
  angular:
    patterns: ["@angular*"]
    update-types: ["minor", "patch"]
  testing:
    patterns: ["jest*", "@testing-library*", "ts-jest"]

For Security Updates

groups:
  security-patches:
    applies-to: security-updates
    patterns: ["*"]
    update-types: ["patch", "minor"]

Key behaviors:

• Dependencies matching multiple groups go to the first match
• applies-to defaults to version-updates when absent
• Ungrouped dependencies get individual PRs

Multi-Ecosystem Groups

Combine updates across different package ecosystems into a single PR:

version: 2

multi-ecosystem-groups:
  infrastructure:
    schedule:
      interval: "weekly"
    labels: ["infrastructure", "dependencies"]

updates:
  - package-ecosystem: "docker"
    directory: "/"
    patterns: ["nginx", "redis"]
    multi-ecosystem-group: "infrastructure"

  - package-ecosystem: "terraform"
    directory: "/"
    patterns: ["aws*"]
    multi-ecosystem-group: "infrastructure"

The patterns key is required when using multi-ecosystem-group.

PR Customization

Labels

labels:
  - "dependencies"
  - "npm"

Set labels: [] to disable all labels including defaults. SemVer labels (major, minor, patch) are always applied if present in the repo.

Commit Messages

commit-message:
  prefix: "deps"
  prefix-development: "deps-dev"
  include: "scope"  # adds deps/deps-dev scope after prefix

Assignees and Milestones

assignees: ["security-team-lead"]
milestone: 4  # numeric ID from milestone URL

Branch Name Separator

pull-request-branch-name:
  separator: "-"  # default is /

Target Branch

target-branch: "develop"  # PRs target this instead of default branch

Note: When target-branch is set, security updates still target the default branch; all ecosystem config only applies to version updates.

Schedule Optimization

Intervals

Supported: daily, weekly, monthly, quarterly, semiannually, yearly, cron

schedule:
  interval: "weekly"
  day: "monday"         # for weekly only
  time: "09:00"         # HH:MM format
  timezone: "America/New_York"

Cron Expressions

schedule:
  interval: "cron"
  cronjob: "0 9 * * 1"  # Every Monday at 9 AM

Cooldown Periods

Delay updates for newly released versions to avoid early-adopter issues:

cooldown:
  default-days: 5
  semver-major-days: 30
  semver-minor-days: 7
  semver-patch-days: 3
  include: ["*"]
  exclude: ["critical-lib"]

Cooldown applies to version updates only, not security updates.

Security Updates Configuration

Enable via Repository Settings

Settings → Advanced Security → Enable Dependabot alerts, security updates, and grouped security updates.

Group Security Updates in YAML

groups:
  security-patches:
    applies-to: security-updates
    patterns: ["*"]
    update-types: ["patch", "minor"]

Disable Version Updates (Security Only)

open-pull-requests-limit: 0  # disables version update PRs

Auto-Triage Rules

GitHub presets auto-dismiss low-impact alerts for development dependencies. Custom rules can filter by severity, package name, CWE, and more. Configure in repository Settings → Advanced Security.

PR Comment Commands

Interact with Dependabot PRs using @dependabot comments.

Note: As of January 2026, merge/close/reopen commands have been deprecated. Use GitHub's native UI, CLI (gh pr merge), or auto-merge instead.

For grouped PRs, additional commands:

• @dependabot ignore DEPENDENCY_NAME — ignore specific dependency in group
• @dependabot unignore DEPENDENCY_NAME — clear ignores, reopen with updates
• @dependabot unignore * — clear all ignores for all dependencies in group
• @dependabot show DEPENDENCY_NAME ignore conditions — display current ignores

For the complete command reference, see references/pr-commands.md.

Ignore and Allow Rules

Ignore Specific Dependencies

ignore:
  - dependency-name: "lodash"
  - dependency-name: "@types/node"
    update-types: ["version-update:semver-patch"]
  - dependency-name: "express"
    versions: ["5.x"]

Allow Only Specific Types

allow:
  - dependency-type: "production"
  - dependency-name: "express"

Rule: If a dependency matches both allow and ignore, it is ignored.

Exclude Paths

exclude-paths:
  - "vendor/**"
  - "test/fixtures/**"

Advanced Options

Versioning Strategy

Controls how Dependabot edits version constraints:

Rebase Strategy

rebase-strategy: "disabled"  # stop auto-rebasing

Allow rebase over extra commits by including [dependabot skip] in commit messages.

Open PR Limit

open-pull-requests-limit: 10  # default is 5 for version, 10 for security

Set to 0 to disable version updates entirely.

Private Registries

registries:
  npm-private:
    type: npm-registry
    url: https://npm.example.com
    token: ${{secrets.NPM_TOKEN}}

updates:
  - package-ecosystem: "npm"
    directory: "/"
    registries:
      - npm-private

FAQ

Can I have multiple dependabot.yml files? No. GitHub supports exactly one file at .github/dependabot.yml. Use multiple updates entries within that file for different ecosystems and directories.

Does Dependabot support pnpm? Yes. Use package-ecosystem: "npm" — Dependabot detects pnpm-lock.yaml automatically.

How do I reduce PR noise in a monorepo? Use groups to batch updates, directories with globs for coverage, and group-by: dependency-name for cross-directory grouping. Consider monthly or quarterly intervals for low-priority ecosystems.

How do I handle dependencies outside the workspace? Create a separate ecosystem entry with its own directory pointing to that location.

Pre-Commit Dependency Scanning via AI Coding Agents

For scanning code changes for vulnerable dependencies inside an AI coding agent before committing, the GitHub MCP Server's dependabot toolset can check your dependency additions against the GitHub Advisory Database and return structured results with affected packages, severity, and recommended fixed versions. For more thorough post-commit checks, it can also run the Dependabot CLI locally to diff dependency graphs before and after your changes.

Install the Advanced Security plugin which provides dedicated dependency scanning tools and the /dependency-scanning skill.

GitHub Copilot CLI (shell):

# Enable the dependabot toolset for the GitHub MCP Server
copilot --add-github-mcp-toolset dependabot

GitHub Copilot CLI (inside copilot):

> /plugin install advanced-security@copilot-plugins

Visual Studio Code:

• Add "X-MCP-Toolsets": "dependabot" to your GitHub MCP Server headers, or pick Dependabot from the toolset selector in Copilot Chat
• Install the advanced-security plugin, then use /dependency-scanning in Copilot Chat

Example prompt:

Scan the dependencies I added on this branch for known vulnerabilities and tell me which versions to upgrade to before I commit.

See: Advanced Security Plugin — Dependency Scanning Skill

Announced in Dependency scanning with GitHub MCP Server is in public preview (May 2026)

Resources

• references/dependabot-yml-reference.md — Complete YAML options reference
• references/pr-commands.md — Full PR comment commands reference
• references/example-configs.md — Real-world configuration examples