diff --git a/.github/workflows/mcp-diff.yml b/.github/workflows/mcp-diff.yml
index 9c9c34b3a..fb2a555bf 100644
--- a/.github/workflows/mcp-diff.yml
+++ b/.github/workflows/mcp-diff.yml
@@ -20,7 +20,7 @@ jobs:
           fetch-depth: 0
 
       - name: Run MCP Server Diff
-        uses: SamMorrowDrums/mcp-server-diff@v2
+        uses: SamMorrowDrums/mcp-server-diff@v2.2.0
         with:
           setup_go: "true"
           install_command: go mod download
@@ -35,8 +35,10 @@ jobs:
               {"name": "read-only+dynamic", "args": "--read-only --dynamic-toolsets"},
               {"name": "toolsets-repos", "args": "--toolsets=repos"},
               {"name": "toolsets-issues", "args": "--toolsets=issues"},
+              {"name": "toolsets-context", "args": "--toolsets=context"},
               {"name": "toolsets-pull_requests", "args": "--toolsets=pull_requests"},
               {"name": "toolsets-repos,issues", "args": "--toolsets=repos,issues"},
+              {"name": "toolsets-issues,context", "args": "--toolsets=issues,context"},
               {"name": "toolsets-all", "args": "--toolsets=all"},
               {"name": "tools-get_me", "args": "--tools=get_me"},
               {"name": "tools-get_me,list_issues", "args": "--tools=get_me,list_issues"},
diff --git a/pkg/inventory/instructions.go b/pkg/inventory/instructions.go
index e4524eb43..02e90cd20 100644
--- a/pkg/inventory/instructions.go
+++ b/pkg/inventory/instructions.go
@@ -31,7 +31,7 @@ Tool usage guidance:
 	instructions = append(instructions, baseInstruction)
 
 	// Collect instructions from each enabled toolset
-	for _, toolset := range inv.AvailableToolsets() {
+	for _, toolset := range inv.EnabledToolsets() {
 		if toolset.InstructionsFunc != nil {
 			if toolsetInstructions := toolset.InstructionsFunc(inv); toolsetInstructions != "" {
 				instructions = append(instructions, toolsetInstructions)
diff --git a/pkg/inventory/instructions_test.go b/pkg/inventory/instructions_test.go
index 7a347c1e2..e8e369b3d 100644
--- a/pkg/inventory/instructions_test.go
+++ b/pkg/inventory/instructions_test.go
@@ -7,6 +7,7 @@ import (
 )
 
 // createTestInventory creates an inventory with the specified toolsets for testing.
+// All toolsets are enabled by default using WithToolsets([]string{"all"}).
 func createTestInventory(toolsets []ToolsetMetadata) *Inventory {
 	// Create tools for each toolset so they show up in AvailableToolsets()
 	var tools []ServerTool
@@ -18,6 +19,7 @@ func createTestInventory(toolsets []ToolsetMetadata) *Inventory {
 
 	inv, _ := NewBuilder().
 		SetTools(tools).
+		WithToolsets([]string{"all"}).
 		Build()
 
 	return inv
@@ -203,3 +205,61 @@ func TestToolsetInstructionsFunc(t *testing.T) {
 		})
 	}
 }
+
+// TestGenerateInstructionsOnlyEnabledToolsets verifies that generateInstructions
+// only includes instructions from enabled toolsets, not all available toolsets.
+// This is a regression test for https://github.com/github/github-mcp-server/issues/1897
+func TestGenerateInstructionsOnlyEnabledToolsets(t *testing.T) {
+	// Create tools for multiple toolsets
+	reposToolset := ToolsetMetadata{
+		ID:          "repos",
+		Description: "Repository tools",
+		InstructionsFunc: func(_ *Inventory) string {
+			return "REPOS_INSTRUCTIONS"
+		},
+	}
+	issuesToolset := ToolsetMetadata{
+		ID:          "issues",
+		Description: "Issue tools",
+		InstructionsFunc: func(_ *Inventory) string {
+			return "ISSUES_INSTRUCTIONS"
+		},
+	}
+	prsToolset := ToolsetMetadata{
+		ID:          "pull_requests",
+		Description: "PR tools",
+		InstructionsFunc: func(_ *Inventory) string {
+			return "PRS_INSTRUCTIONS"
+		},
+	}
+
+	tools := []ServerTool{
+		{Toolset: reposToolset},
+		{Toolset: issuesToolset},
+		{Toolset: prsToolset},
+	}
+
+	// Build inventory with only "repos" toolset enabled
+	inv, err := NewBuilder().
+		SetTools(tools).
+		WithToolsets([]string{"repos"}).
+		Build()
+	if err != nil {
+		t.Fatalf("Failed to build inventory: %v", err)
+	}
+
+	result := generateInstructions(inv)
+
+	// Should contain instructions from enabled toolset
+	if !strings.Contains(result, "REPOS_INSTRUCTIONS") {
+		t.Errorf("Expected instructions to contain 'REPOS_INSTRUCTIONS' for enabled toolset, but it did not. Result: %s", result)
+	}
+
+	// Should NOT contain instructions from non-enabled toolsets
+	if strings.Contains(result, "ISSUES_INSTRUCTIONS") {
+		t.Errorf("Did not expect instructions to contain 'ISSUES_INSTRUCTIONS' for disabled toolset, but it did. Result: %s", result)
+	}
+	if strings.Contains(result, "PRS_INSTRUCTIONS") {
+		t.Errorf("Did not expect instructions to contain 'PRS_INSTRUCTIONS' for disabled toolset, but it did. Result: %s", result)
+	}
+}
diff --git a/pkg/inventory/registry.go b/pkg/inventory/registry.go
index e4113b452..e2cd3a9e6 100644
--- a/pkg/inventory/registry.go
+++ b/pkg/inventory/registry.go
@@ -295,6 +295,28 @@ func (r *Inventory) AvailableToolsets(exclude ...ToolsetID) []ToolsetMetadata {
 	return result
 }
 
+// EnabledToolsets returns the unique toolsets that are enabled based on current filters.
+// This is similar to AvailableToolsets but respects the enabledToolsets filter.
+// Returns toolsets in sorted order by toolset ID.
+func (r *Inventory) EnabledToolsets() []ToolsetMetadata {
+	// Get all available toolsets first (already sorted by ID)
+	allToolsets := r.AvailableToolsets()
+
+	// If no filter is set, all toolsets are enabled
+	if r.enabledToolsets == nil {
+		return allToolsets
+	}
+
+	// Filter to only enabled toolsets
+	var result []ToolsetMetadata
+	for _, ts := range allToolsets {
+		if r.enabledToolsets[ts.ID] {
+			result = append(result, ts)
+		}
+	}
+	return result
+}
+
 func (r *Inventory) Instructions() string {
 	return r.instructions
 }