diff --git a/packages/core/src/execution-engine/partial-execution-utils/__tests__/clean-run-data.test.ts b/packages/core/src/execution-engine/partial-execution-utils/__tests__/clean-run-data.test.ts
index 7de648e6fd8c5..77611703f0ddc 100644
--- a/packages/core/src/execution-engine/partial-execution-utils/__tests__/clean-run-data.test.ts
+++ b/packages/core/src/execution-engine/partial-execution-utils/__tests__/clean-run-data.test.ts
@@ -1,4 +1,15 @@
-import type { IRunData } from 'n8n-workflow';
+// NOTE: Diagrams in this file have been created with https://asciiflow.com/#/
+// If you update the tests, please update the diagrams as well.
+// If you add a test, please create a new diagram.
+//
+// Map
+// 0  means the output has no run data
+// 1  means the output has run data
+// ►► denotes the node that the user wants to execute to
+// XX denotes that the node is disabled
+// PD denotes that the node has pinned data
+
+import { NodeConnectionType, type IRunData } from 'n8n-workflow';
 
 import { createNodeData, toITaskData } from './helpers';
 import { cleanRunData } from '../clean-run-data';
@@ -111,4 +122,73 @@ describe('cleanRunData', () => {
 			[node1.name]: [toITaskData([{ data: { value: 1 } }])],
 		});
 	});
+
+	//  ┌─────┐     ┌────────┐
+	//  │node1├─────►rootNode│
+	//  └─────┘     └───▲────┘
+	//                  │
+	//              ┌───┴───┐
+	//              │subNode│
+	//              └───────┘
+	test('removes run data of sub nodes when the start node is a root node', () => {
+		// ARRANGE
+		const node1 = createNodeData({ name: 'Node1' });
+		const rootNode = createNodeData({ name: 'Root Node' });
+		const subNode = createNodeData({ name: 'Sub Node' });
+		const graph = new DirectedGraph()
+			.addNodes(node1, rootNode, subNode)
+			.addConnections(
+				{ from: node1, to: rootNode },
+				{ from: subNode, to: rootNode, type: NodeConnectionType.AiLanguageModel },
+			);
+		const runData: IRunData = {
+			[node1.name]: [toITaskData([{ data: { value: 1 } }])],
+			[rootNode.name]: [toITaskData([{ data: { value: 2 } }])],
+			[subNode.name]: [toITaskData([{ data: { value: 3 } }])],
+		};
+
+		// ACT
+		const newRunData = cleanRunData(runData, graph, new Set([rootNode]));
+
+		// ASSERT
+		expect(newRunData).toEqual({
+			[node1.name]: [toITaskData([{ data: { value: 1 } }])],
+		});
+	});
+
+	// ┌─────┐   ┌─────┐    ┌────────┐
+	// │node1├───►node2├────►rootNode│
+	// └─────┘   └─────┘    └───▲────┘
+	//                          │
+	//                      ┌───┴───┐
+	//                      │subNode│
+	//                      └───────┘
+	test('removes run data of sub nodes for root nodes downstream of the start node', () => {
+		// ARRANGE
+		const node1 = createNodeData({ name: 'Node1' });
+		const node2 = createNodeData({ name: 'Node2' });
+		const rootNode = createNodeData({ name: 'Root Node' });
+		const subNode = createNodeData({ name: 'Sub Node' });
+		const graph = new DirectedGraph()
+			.addNodes(node1, node2, rootNode, subNode)
+			.addConnections(
+				{ from: node1, to: node2 },
+				{ from: node2, to: rootNode },
+				{ from: subNode, to: rootNode, type: NodeConnectionType.AiLanguageModel },
+			);
+		const runData: IRunData = {
+			[node1.name]: [toITaskData([{ data: { value: 1 } }])],
+			[node2.name]: [toITaskData([{ data: { value: 1 } }])],
+			[rootNode.name]: [toITaskData([{ data: { value: 2 } }])],
+			[subNode.name]: [toITaskData([{ data: { value: 3 } }])],
+		};
+
+		// ACT
+		const newRunData = cleanRunData(runData, graph, new Set([node2]));
+
+		// ASSERT
+		expect(newRunData).toEqual({
+			[node1.name]: [toITaskData([{ data: { value: 1 } }])],
+		});
+	});
 });
diff --git a/packages/core/src/execution-engine/partial-execution-utils/clean-run-data.ts b/packages/core/src/execution-engine/partial-execution-utils/clean-run-data.ts
index 78d08acd9b53d..a6cf7f0b27273 100644
--- a/packages/core/src/execution-engine/partial-execution-utils/clean-run-data.ts
+++ b/packages/core/src/execution-engine/partial-execution-utils/clean-run-data.ts
@@ -1,4 +1,4 @@
-import type { INode, IRunData } from 'n8n-workflow';
+import { NodeConnectionType, type INode, type IRunData } from 'n8n-workflow';
 
 import type { DirectedGraph } from './directed-graph';
 
@@ -16,10 +16,22 @@ export function cleanRunData(
 
 	for (const startNode of startNodes) {
 		delete newRunData[startNode.name];
+
 		const children = graph.getChildren(startNode);
+		for (const node of [startNode, ...children]) {
+			delete newRunData[node.name];
+
+			// Delete runData for subNodes
+			const subNodeConnections = graph.getParentConnections(node);
+			for (const subNodeConnection of subNodeConnections) {
+				// Sub nodes never use the Main connection type, so this filters our
+				// the connection that goes upstream of the startNode.
+				if (subNodeConnection.type === NodeConnectionType.Main) {
+					continue;
+				}
 
-		for (const child of children) {
-			delete newRunData[child.name];
+				delete newRunData[subNodeConnection.from.name];
+			}
 		}
 	}