diff --git a/changelog.md b/changelog.md
index 3ba6779..0f914e7 100644
--- a/changelog.md
+++ b/changelog.md
@@ -16,6 +16,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `AIService.diagnose()` now uses the `static.AI_DIR` constant (`.agents`) instead of the hardcoded `/.ai` path
   - `coldbox ai uninstall` now correctly checks, removes, and references the `.agents` directory
 - `coldbox ai skills add slug --list` was not working.
+- **`coldbox ai skills remove` reinstalling removed skills during refresh**
+  - When a skill was removed via `coldbox ai skills remove`, the subsequent agent config regeneration step (`refresh()`) would detect the skill as "missing" (because its module dependency was still present in `box.json`) and immediately reinstall it
+  - Removed skills are now tracked in a new `manifest.excludes[]` array so that `refresh()` will never auto-reinstall them
+  - Explicitly re-installing a previously excluded skill via `coldbox ai skills install` lifts the exclusion and restores normal auto-management
 
 ### Added
 
diff --git a/models/SkillManager.cfc b/models/SkillManager.cfc
index c64ad8a..dabd32e 100644
--- a/models/SkillManager.cfc
+++ b/models/SkillManager.cfc
@@ -186,6 +186,9 @@ component singleton {
 		// Ensure customSkills key exists (backwards compatibility with old manifests)
 		ensureCustomSkillsSection( arguments.manifest )
 
+		// Ensure excludes key exists (backwards compatibility with old manifests)
+		ensureExcludesSection( arguments.manifest )
+
 		// ------------------------------------------------------------------
 		// 0. Install missing desired skills (core + module) not yet in manifest
 		// ------------------------------------------------------------------
@@ -195,6 +198,10 @@ component singleton {
 		);
 
 		var missingDesiredSkills = desiredTargets.filter( ( t ) => {
+			// Skip skills the user has explicitly excluded
+			if ( arguments.manifest.excludes.findNoCase( t.name ) ) {
+				return false;
+			}
 			return !manifest.skills
 				.filter( ( s ) => {
 					return ( s.owner == t.owner && s.repo == t.repo && s.slug == t.slug );
@@ -828,6 +835,13 @@ component singleton {
 		if ( structKeyExists( manifest, "customSkills" ) ) {
 			manifest.customSkills = manifest.customSkills.filter( ( s ) => s.name != name )
 		}
+
+		// Track the explicit exclusion so refresh() does not auto-reinstall it
+		ensureExcludesSection( manifest )
+		if ( !manifest.excludes.findNoCase( arguments.name ) ) {
+			manifest.excludes.append( arguments.name )
+		}
+
 		variables.aiService.saveManifest( arguments.directory, manifest )
 
 		return true
@@ -1345,6 +1359,10 @@ component singleton {
 			arguments.manifest.skills.append( entry )
 		}
 
+		// If this skill was previously excluded, lift the exclusion now that it is being explicitly installed
+		ensureExcludesSection( arguments.manifest )
+		arguments.manifest.excludes = arguments.manifest.excludes.filter( ( excludedName ) => !excludedName.equalsIgnoreCase( resolvedName ) )
+
 		return resolvedName
 	}
 
@@ -1397,6 +1415,20 @@ component singleton {
 		}
 	}
 
+	/**
+	 * Ensure manifest has an excludes array (backwards compatibility).
+	 * The excludes array holds skill names that the user explicitly removed and
+	 * should never be auto-reinstalled by refresh().
+	 * Mutates manifest in place.
+	 *
+	 * @manifest The manifest struct to ensure has an excludes key
+	 */
+	private function ensureExcludesSection( required struct manifest ){
+		if ( !structKeyExists( arguments.manifest, "excludes" ) ) {
+			arguments.manifest[ "excludes" ] = []
+		}
+	}
+
 	/**
 	 * Delete a skill directory under .ai/skills/ if it exists.
 	 *