diff --git a/pkg/github/tools_validation_test.go b/pkg/github/tools_validation_test.go
index 90e3c744c..8100ce8fb 100644
--- a/pkg/github/tools_validation_test.go
+++ b/pkg/github/tools_validation_test.go
@@ -184,3 +184,143 @@ func TestToolsetMetadataConsistency(t *testing.T) {
 		}
 	}
 }
+
+// TestFeatureFlaggedToolsAreMutuallyExclusive validates that when multiple tools share
+// the same name with different feature flags, they are properly configured to ensure:
+// - At most one tool variant is active for any given feature flag state
+// - A tool shows up when it should (no omissions)
+// - No tool shows up when it shouldn't (no incorrect activations)
+// - No duplicate tool names are active simultaneously
+// This prevents issues where filtering returns the wrong variant or no variant at all.
+func TestFeatureFlaggedToolsAreMutuallyExclusive(t *testing.T) {
+	tools := AllTools(stubTranslation)
+
+	// Group tools by name
+	toolsByName := make(map[string][]inventory.ServerTool)
+	for _, tool := range tools {
+		toolsByName[tool.Tool.Name] = append(toolsByName[tool.Tool.Name], tool)
+	}
+
+	// Check each group of tools with the same name
+	for name, group := range toolsByName {
+		if len(group) <= 1 {
+			continue // Single tool, no conflict possible
+		}
+
+		// Skip explicitly allowed duplicates (like get_label)
+		if name == "get_label" {
+			continue
+		}
+
+		t.Run(name, func(t *testing.T) {
+			// All tools with the same name must have feature flags
+			for i, tool := range group {
+				hasFlags := tool.FeatureFlagEnable != "" || tool.FeatureFlagDisable != ""
+				assert.True(t, hasFlags,
+					"Tool %q (variant %d/%d) shares a name with other tools but has no feature flags",
+					name, i+1, len(group))
+			}
+
+			// Verify mutual exclusivity: collect all flags used
+			enableFlags := make(map[string]bool)
+			disableFlags := make(map[string]bool)
+
+			for _, tool := range group {
+				if tool.FeatureFlagEnable != "" {
+					enableFlags[tool.FeatureFlagEnable] = true
+				}
+				if tool.FeatureFlagDisable != "" {
+					disableFlags[tool.FeatureFlagDisable] = true
+				}
+			}
+
+			// For proper mutual exclusivity, we expect:
+			// - Same flag name used in both FeatureFlagEnable and FeatureFlagDisable
+			// - This ensures only one variant is active at a time
+			if len(group) == 2 {
+				// Most common case: two variants controlled by one flag
+				var flagName string
+				for flag := range enableFlags {
+					flagName = flag
+					break
+				}
+				for flag := range disableFlags {
+					if flagName == "" {
+						flagName = flag
+					}
+				}
+
+				if flagName != "" {
+					assert.True(t, enableFlags[flagName] || disableFlags[flagName],
+						"Tools sharing name %q should use the same flag for mutual exclusivity", name)
+
+					// Verify exactly one tool has FeatureFlagEnable=flagName and one has FeatureFlagDisable=flagName
+					enableCount := 0
+					disableCount := 0
+					for _, tool := range group {
+						if tool.FeatureFlagEnable == flagName {
+							enableCount++
+						}
+						if tool.FeatureFlagDisable == flagName {
+							disableCount++
+						}
+					}
+
+					// We should have at least one of each for proper mutual exclusivity
+					assert.True(t, enableCount > 0 || disableCount > 0,
+						"Tools sharing name %q should have proper feature flag configuration", name)
+				}
+			}
+
+			// Additional safety check: ensure no two tools could be enabled simultaneously
+			// by testing all possible flag states
+			testFlagStates := []map[string]bool{
+				{}, // All flags off
+				// We'll add specific flag combinations based on what flags we found
+			}
+
+			// Add test cases for each unique flag
+			allFlags := make(map[string]bool)
+			for flag := range enableFlags {
+				allFlags[flag] = true
+			}
+			for flag := range disableFlags {
+				allFlags[flag] = true
+			}
+
+			for flag := range allFlags {
+				testFlagStates = append(testFlagStates, map[string]bool{flag: true})
+			}
+
+			// Test each flag state
+			for stateIdx, flagState := range testFlagStates {
+				enabledCount := 0
+				for _, tool := range group {
+					enabled := true
+
+					// Check FeatureFlagEnable - tool requires this flag to be ON
+					if tool.FeatureFlagEnable != "" {
+						if !flagState[tool.FeatureFlagEnable] {
+							enabled = false
+						}
+					}
+
+					// Check FeatureFlagDisable - tool is disabled if this flag is ON
+					if tool.FeatureFlagDisable != "" {
+						if flagState[tool.FeatureFlagDisable] {
+							enabled = false
+						}
+					}
+
+					if enabled {
+						enabledCount++
+					}
+				}
+
+				assert.LessOrEqual(t, enabledCount, 1,
+					"Flag state %d for tool %q: At most one variant should be enabled (found %d enabled)",
+					stateIdx, name, enabledCount)
+			}
+		})
+	}
+}
diff --git a/pkg/inventory/registry_test.go b/pkg/inventory/registry_test.go
index 742ad3646..9313944d0 100644
--- a/pkg/inventory/registry_test.go
+++ b/pkg/inventory/registry_test.go
@@ -1688,3 +1688,250 @@ func TestForMCPRequest_ToolsCall_FeatureFlaggedVariants(t *testing.T) {
 			availableOn[0].FeatureFlagEnable, availableOn[0].FeatureFlagDisable)
 	}
 }
+
+// TestToolsList_WithFeatureFlags validates that tools/list returns only the tools
+// available based on the current feature flag state, without duplicates or omissions
+func TestToolsList_WithFeatureFlags(t *testing.T) {
+	// Create tools with various feature flag configurations
+	// These are properly mutually exclusive
+	tools := []ServerTool{
+		mockToolWithFlags("tool_a", "test", true, "", "flag_x"), // disabled when flag_x is ON
+		mockToolWithFlags("tool_a", "test", true, "flag_x", ""), // enabled when flag_x is ON
+		mockToolWithFlags("tool_b", "test", true, "flag_y", ""), // enabled only when flag_y is ON
+		mockToolWithFlags("tool_c", "test", true, "", "flag_z"), // disabled when flag_z is ON
+		mockToolWithFlags("tool_c", "test", true, "flag_z", ""), // enabled when flag_z is ON
+		mockTool("tool_d", "test", true),                        // always enabled (no flags)
+	}
+
+	testCases := []struct {
+		name          string
+		flagStates    map[string]bool
+		expectedTools []string // tool names that should be available
+	}{
+		{
+			name:          "All flags OFF",
+			flagStates:    map[string]bool{},
+			expectedTools: []string{"tool_a", "tool_c", "tool_d"},
+		},
+		{
+			name:          "flag_x ON",
+			flagStates:    map[string]bool{"flag_x": true},
+			expectedTools: []string{"tool_a", "tool_c", "tool_d"},
+		},
+		{
+			name:          "flag_y ON",
+			flagStates:    map[string]bool{"flag_y": true},
+			expectedTools: []string{"tool_a", "tool_b", "tool_c", "tool_d"},
+		},
+		{
+			name:          "flag_z ON",
+			flagStates:    map[string]bool{"flag_z": true},
+			expectedTools: []string{"tool_a", "tool_c", "tool_d"},
+		},
+		{
+			name:          "flag_x and flag_y ON",
+			flagStates:    map[string]bool{"flag_x": true, "flag_y": true},
+			expectedTools: []string{"tool_a", "tool_b", "tool_c", "tool_d"},
+		},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.name, func(t *testing.T) {
+			// Create feature checker that returns the flag states for this test case
+			checker := func(_ context.Context, flag string) (bool, error) {
+				return tc.flagStates[flag], nil
+			}
+
+			reg := NewBuilder().
+				SetTools(tools).
+				WithToolsets([]string{"all"}).
+				WithFeatureChecker(checker).
+				Build()
+
+			// Test tools/list endpoint
+			listReg := reg.ForMCPRequest(MCPMethodToolsList, "")
+			available := listReg.AvailableTools(context.Background())
+
+			// Collect available tool names
+			availableNames := make(map[string]int)
+			for _, tool := range available {
+				availableNames[tool.Tool.Name]++
+			}
+
+			// Verify expected tools are present
+			for _, expectedName := range tc.expectedTools {
+				count, found := availableNames[expectedName]
+				if !found {
+					t.Errorf("Expected tool %q not found in available tools", expectedName)
+				} else if count > 1 {
+					t.Errorf("Tool %q appears %d times (should appear only once)", expectedName, count)
+				}
+			}
+
+			// Verify no unexpected tools
+			if len(availableNames) != len(tc.expectedTools) {
+				t.Errorf("Expected %d tools, got %d: %v", len(tc.expectedTools), len(availableNames), availableNames)
+			}
+
+			// Verify no duplicate tool names in the result
+			for name, count := range availableNames {
+				if count > 1 {
+					t.Errorf("Duplicate tool name %q appears %d times", name, count)
+				}
+			}
+		})
+	}
+}
+
+// TestToolsCall_WithFeatureFlags validates that tools/call (ForMCPRequest with specific tool)
+// returns the correct tool variant based on feature flags
+func TestToolsCall_WithFeatureFlags(t *testing.T) {
+	tools := []ServerTool{
+		mockToolWithFlags("shared_tool", "test", true, "", "feature_flag"), // OLD: disabled when feature_flag is ON
+		mockToolWithFlags("shared_tool", "test", true, "feature_flag", ""), // NEW: enabled when feature_flag is ON
+		mockTool("other_tool", "test", true),
+	}
+
+	testCases := []struct {
+		name              string
+		toolName          string
+		featureFlagOn     bool
+		expectToolCount   int
+		expectEnableFlag  string
+		expectDisableFlag string
+	}{
+		{
+			name:              "Call shared_tool with flag OFF - should get old variant",
+			toolName:          "shared_tool",
+			featureFlagOn:     false,
+			expectToolCount:   1,
+			expectEnableFlag:  "",
+			expectDisableFlag: "feature_flag",
+		},
+		{
+			name:              "Call shared_tool with flag ON - should get new variant",
+			toolName:          "shared_tool",
+			featureFlagOn:     true,
+			expectToolCount:   1,
+			expectEnableFlag:  "feature_flag",
+			expectDisableFlag: "",
+		},
+		{
+			name:              "Call other_tool - always available",
+			toolName:          "other_tool",
+			featureFlagOn:     false,
+			expectToolCount:   1,
+			expectEnableFlag:  "",
+			expectDisableFlag: "",
+		},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.name, func(t *testing.T) {
+			var checker FeatureFlagChecker
+			if tc.featureFlagOn {
+				checker = func(_ context.Context, flag string) (bool, error) {
+					return flag == "feature_flag", nil
+				}
+			} else {
+				checker = func(_ context.Context, _ string) (bool, error) {
+					return false, nil
+				}
+			}
+
+			reg := NewBuilder().
+				SetTools(tools).
+				WithToolsets([]string{"all"}).
+				WithFeatureChecker(checker).
+				Build()
+
+			// Test tools/call endpoint
+			callReg := reg.ForMCPRequest(MCPMethodToolsCall, tc.toolName)
+			available := callReg.AvailableTools(context.Background())
+
+			if len(available) != tc.expectToolCount {
+				t.Fatalf("Expected %d tool(s), got %d", tc.expectToolCount, len(available))
+			}
+
+			if tc.expectToolCount > 0 {
+				tool := available[0]
+				if tool.Tool.Name != tc.toolName {
+					t.Errorf("Expected tool name %q, got %q", tc.toolName, tool.Tool.Name)
+				}
+				if tool.FeatureFlagEnable != tc.expectEnableFlag {
+					t.Errorf("Expected FeatureFlagEnable=%q, got %q", tc.expectEnableFlag, tool.FeatureFlagEnable)
+				}
+				if tool.FeatureFlagDisable != tc.expectDisableFlag {
+					t.Errorf("Expected FeatureFlagDisable=%q, got %q", tc.expectDisableFlag, tool.FeatureFlagDisable)
+				}
+			}
+		})
+	}
+}
+
+// TestNoDuplicateToolsInAnyFeatureFlagCombination validates that no matter what
+// combination of feature flags is enabled, we never have duplicate tool names in
+// the available tools list
+func TestNoDuplicateToolsInAnyFeatureFlagCombination(t *testing.T) {
+	tools := []ServerTool{
+		// Simulate real tools with feature flags
+		mockToolWithFlags("actions_list", "test", true, "", "consolidated"),
+		mockToolWithFlags("actions_list", "test", true, "consolidated", ""),
+		mockToolWithFlags("actions_get", "test", true, "", "consolidated"),
+		mockToolWithFlags("actions_get", "test", true, "consolidated", ""),
+		mockToolWithFlags("get_job_logs", "test", true, "", "consolidated"),
+		mockToolWithFlags("get_job_logs", "test", true, "consolidated", ""),
+		mockTool("regular_tool", "test", true),
+		mockToolWithFlags("feature_tool", "test", true, "other_flag", ""),
+	}
+
+	// Test all combinations of feature flags
+	flags := []string{"consolidated", "other_flag"}
+
+	// Generate all possible combinations of flags (2^n combinations)
+	numCombinations := 1 << len(flags)
+
+	for i := 0; i < numCombinations; i++ {
+		flagStates := make(map[string]bool)
+		var testName string
+		for j, flag := range flags {
+			isOn := (i & (1 << j)) != 0
+			flagStates[flag] = isOn
+			if isOn {
+				if testName != "" {
+					testName += "_"
+				}
+				testName += flag
+			}
+		}
+		if testName == "" {
+			testName = "no_flags"
+		}
+
+		t.Run(testName, func(t *testing.T) {
+			checker := func(_ context.Context, flag string) (bool, error) {
+				return flagStates[flag], nil
+			}
+
+			reg := NewBuilder().
+				SetTools(tools).
+				WithToolsets([]string{"all"}).
+				WithFeatureChecker(checker).
+				Build()
+
+			available := reg.AvailableTools(context.Background())
+
+			// Check for duplicates
+			seen := make(map[string]int)
+			for _, tool := range available {
+				seen[tool.Tool.Name]++
+			}
+
+			for name, count := range seen {
+				if count > 1 {
+					t.Errorf("Duplicate tool %q appears %d times with flag state: %v", name, count, flagStates)
+				}
+			}
+		})
+	}
+}