diff --git a/internal/agent/canvas/scheduler.go b/internal/agent/canvas/scheduler.go
index 7936ce3a17..67e0971625 100644
--- a/internal/agent/canvas/scheduler.go
+++ b/internal/agent/canvas/scheduler.go
@@ -742,7 +742,15 @@ func BuildWorkflow(ctx context.Context, c *Canvas) (*compose.Workflow[map[string
 	// (a downstream that's also a sub-graph member doesn't count — that
 	// node is part of the loop's body, not the outer graph's edge).
 	terminals := make([]string, 0, len(c.Components))
+	roots := make(map[string]bool)
+	entries := make(map[string]bool)
 	for cpnID, comp := range c.Components {
+		if !macroMembers[cpnID] && len(comp.Upstream) == 0 && !first[cpnID] {
+			roots[cpnID] = true
+			if strings.EqualFold(comp.Obj.ComponentName, "Begin") || strings.EqualFold(comp.Obj.ComponentName, "File") {
+				entries[cpnID] = true
+			}
+		}
 		if node, isMacro := macroNodes[cpnID]; isMacro {
 			// Macro parents with no upstream are START nodes. Parents
 			// with upstream had their AddInput wired in Pass 2 already.
@@ -773,6 +781,14 @@ func BuildWorkflow(ctx context.Context, c *Canvas) (*compose.Workflow[map[string
 		}
 	}
 
+	if len(entries) > 0 && len(entries) < len(roots) {
+		// Branch pruning skips disconnected roots and their terminal dependencies.
+		wf.AddBranch(compose.START, compose.NewGraphMultiBranch(
+			func(context.Context, map[string]any) (map[string]bool, error) {
+				return entries, nil
+			}, roots))
+	}
+
 	if err := wireWorkflowTerminals(wf, terminals, "", true); err != nil {
 		return nil, err
 	}
diff --git a/internal/service/agent_run_e2e_test.go b/internal/service/agent_run_e2e_test.go
index 49720712c4..fa7e443061 100644
--- a/internal/service/agent_run_e2e_test.go
+++ b/internal/service/agent_run_e2e_test.go
@@ -548,20 +548,21 @@ func TestRunAgent_RealCanvas_WaitForUserResume(t *testing.T) {
 					"component_name": "Begin",
 					"params":         map[string]any{},
 				},
-				"downstream": []any{"message_0"},
+				"downstream": []any{"user_fill_up_0"},
 			},
 			"message_0": map[string]any{
 				"obj": map[string]any{
 					"component_name": "Message",
 					"params":         map[string]any{"text": "got: {{user_fill_up_0@user_input}}"},
 				},
-				"upstream": []any{"begin_0", "user_fill_up_0"},
+				"upstream": []any{"user_fill_up_0"},
 			},
 			"user_fill_up_0": map[string]any{
 				"obj": map[string]any{
 					"component_name": "UserFillUp",
 					"params":         map[string]any{"enable_tips": true},
 				},
+				"upstream":   []any{"begin_0"},
 				"downstream": []any{"message_0"},
 			},
 		},
@@ -782,6 +783,7 @@ func TestRunAgent_RealCanvas_WaitForUserResume_EventSemantics(t *testing.T) {
 					"component_name": "UserFillUp",
 					"params":         map[string]any{"enable_tips": true},
 				},
+				"upstream":   []any{"begin_0"},
 				"downstream": []any{"message_0"},
 			},
 			"message_0": map[string]any{
@@ -789,7 +791,7 @@ func TestRunAgent_RealCanvas_WaitForUserResume_EventSemantics(t *testing.T) {
 					"component_name": "Message",
 					"params":         map[string]any{"text": "got: {{user_fill_up_0@user_input}}"},
 				},
-				"upstream": []any{"begin_0", "user_fill_up_0"},
+				"upstream": []any{"user_fill_up_0"},
 			},
 		},
 		"path": []any{"begin_0", "user_fill_up_0", "message_0"},