diff --git a/src/services/workflow-diff-engine.ts b/src/services/workflow-diff-engine.ts
index 738dc1f..441a3ed 100644
--- a/src/services/workflow-diff-engine.ts
+++ b/src/services/workflow-diff-engine.ts
@@ -648,10 +648,12 @@ export class WorkflowDiffEngine {
     let sourceIndex = operation.sourceIndex ?? 0;
 
     // Smart parameter: branch (for IF nodes)
-    if (operation.branch && !operation.sourceOutput) {
-      // Only apply if sourceOutput not explicitly set
+    // IF nodes use 'main' output with index 0 (true) or 1 (false)
+    if (operation.branch !== undefined && operation.sourceIndex === undefined) {
+      // Only apply if sourceIndex not explicitly set
       if (sourceNode?.type === 'n8n-nodes-base.if') {
-        sourceOutput = operation.branch; // 'true' or 'false'
+        sourceIndex = operation.branch === 'true' ? 0 : 1;
+        // sourceOutput remains 'main' (do not change it)
       }
     }
 
diff --git a/src/types/workflow-diff.ts b/src/types/workflow-diff.ts
index 647f3ca..3ca3639 100644
--- a/src/types/workflow-diff.ts
+++ b/src/types/workflow-diff.ts
@@ -65,8 +65,8 @@ export interface AddConnectionOperation extends DiffOperation {
   sourceIndex?: number; // Default: 0
   targetIndex?: number; // Default: 0
   // Smart parameters for multi-output nodes (Phase 1 UX improvement)
-  branch?: 'true' | 'false'; // For IF nodes: maps to sourceOutput
-  case?: number; // For Switch nodes: maps to sourceIndex
+  branch?: 'true' | 'false'; // For IF nodes: maps to sourceIndex (0=true, 1=false)
+  case?: number; // For Switch/multi-output nodes: maps to sourceIndex
 }
 
 export interface RemoveConnectionOperation extends DiffOperation {
@@ -99,8 +99,8 @@ export interface RewireConnectionOperation extends DiffOperation {
   targetInput?: string;   // Optional: which input type (default: 'main')
   sourceIndex?: number;   // Optional: which source index (default: 0)
   // Smart parameters for multi-output nodes (Phase 1 UX improvement)
-  branch?: 'true' | 'false'; // For IF nodes: maps to sourceOutput
-  case?: number; // For Switch nodes: maps to sourceIndex
+  branch?: 'true' | 'false'; // For IF nodes: maps to sourceIndex (0=true, 1=false)
+  case?: number; // For Switch/multi-output nodes: maps to sourceIndex
 }
 
 // Workflow Metadata Operations
diff --git a/tests/unit/services/workflow-diff-engine.test.ts b/tests/unit/services/workflow-diff-engine.test.ts
index 9fd3c0d..ca1657b 100644
--- a/tests/unit/services/workflow-diff-engine.test.ts
+++ b/tests/unit/services/workflow-diff-engine.test.ts
@@ -1184,9 +1184,10 @@ describe('WorkflowDiffEngine', () => {
       expect(result.success).toBe(true);
       expect(result.workflow).toBeDefined();
 
-      // Should create connection on 'true' output
-      expect(result.workflow!.connections['IF']['true']).toBeDefined();
-      expect(result.workflow!.connections['IF']['true'][0][0].node).toBe('TrueHandler');
+      // Should create connection on 'main' output, index 0 (true branch)
+      expect(result.workflow!.connections['IF']['main']).toBeDefined();
+      expect(result.workflow!.connections['IF']['main'][0]).toBeDefined();
+      expect(result.workflow!.connections['IF']['main'][0][0].node).toBe('TrueHandler');
     });
 
     it('should use branch="false" for IF node connections', async () => {
@@ -1224,9 +1225,10 @@ describe('WorkflowDiffEngine', () => {
 
       expect(result.success).toBe(true);
 
-      // Should create connection on 'false' output
-      expect(result.workflow!.connections['IF']['false']).toBeDefined();
-      expect(result.workflow!.connections['IF']['false'][0][0].node).toBe('FalseHandler');
+      // Should create connection on 'main' output, index 1 (false branch)
+      expect(result.workflow!.connections['IF']['main']).toBeDefined();
+      expect(result.workflow!.connections['IF']['main'][1]).toBeDefined();
+      expect(result.workflow!.connections['IF']['main'][1][0].node).toBe('FalseHandler');
     });
 
     it('should use case parameter for Switch node connections', async () => {
@@ -1360,8 +1362,10 @@ describe('WorkflowDiffEngine', () => {
 
       expect(result.success).toBe(true);
 
-      // Should rewire the true branch
-      expect(result.workflow!.connections['IFRewire']['true'][0][0].node).toBe('NewSuccessHandler');
+      // Should rewire the true branch (main output, index 0)
+      expect(result.workflow!.connections['IFRewire']['main']).toBeDefined();
+      expect(result.workflow!.connections['IFRewire']['main'][0]).toBeDefined();
+      expect(result.workflow!.connections['IFRewire']['main'][0][0].node).toBe('NewSuccessHandler');
     });
 
     it('should use case parameter with rewireConnection', async () => {
@@ -1457,10 +1461,12 @@ describe('WorkflowDiffEngine', () => {
 
       expect(result.success).toBe(true);
 
-      // Should use explicit sourceOutput ('false'), not branch ('true')
+      // Should use explicit sourceOutput ('false'), not smart branch parameter
+      // Note: explicit sourceOutput='false' creates connection on output named 'false'
+      // This is different from branch parameter which maps to sourceIndex
       expect(result.workflow!.connections['IFOverride']['false']).toBeDefined();
       expect(result.workflow!.connections['IFOverride']['false'][0][0].node).toBe('OverrideHandler');
-      expect(result.workflow!.connections['IFOverride']['true']).toBeUndefined();
+      expect(result.workflow!.connections['IFOverride']['main']).toBeUndefined();
     });
 
     it('should not override explicit sourceIndex with case parameter', async () => {