diff --git a/cypress/integration/rendering/flowchart-v2.spec.js b/cypress/integration/rendering/flowchart-v2.spec.js
index 5b358e051f..3eb2a0432a 100644
--- a/cypress/integration/rendering/flowchart-v2.spec.js
+++ b/cypress/integration/rendering/flowchart-v2.spec.js
@@ -760,6 +760,51 @@ A ~~~ B
     );
   });
 
+  it('3258: Should render subgraphs with main graph nodeSpacing and rankSpacing', () => {
+    imgSnapshotTest(
+      `---
+      title: Subgraph nodeSpacing and rankSpacing example
+      ---
+      flowchart LR
+        X --> Y
+        subgraph X
+          direction LR
+          A
+          C
+        end
+        subgraph Y
+          B
+          D
+        end
+      `,
+      { flowchart: { nodeSpacing: 1, rankSpacing: 1 } }
+    );
+  });
+
+  it('3258: Should render subgraphs with large nodeSpacing and rankSpacing', () => {
+    imgSnapshotTest(
+      `---
+      title: Subgraph nodeSpacing and rankSpacing example
+      config:
+        flowchart: 
+          nodeSpacing: 250
+          rankSpacing: 250
+      ---
+      flowchart LR
+        X --> Y
+        subgraph X
+          direction LR
+          A
+          C
+        end
+        subgraph Y
+          B
+          D
+        end
+      `
+    );
+  });
+
   describe('Markdown strings flowchart (#4220)', () => {
     describe('html labels', () => {
       it('With styling and classes', () => {
diff --git a/demos/flowchart.html b/demos/flowchart.html
index 9efdf3aa33..0c71a2bf84 100644
--- a/demos/flowchart.html
+++ b/demos/flowchart.html
@@ -1591,6 +1591,33 @@ <h3>flowchart</h3>
     </pre>
     <hr />
 
+    <pre class="mermaid">
+      ---
+      title: Subgraph nodeSpacing and rankSpacing example
+      config:
+        flowchart:
+          nodeSpacing: 1
+          rankSpacing: 1
+      ---
+
+      flowchart LR
+      
+      X --> Y
+      
+      subgraph X
+        direction LR
+        A
+        C
+      end
+      
+      subgraph Y
+        direction LR
+        B
+        D
+      end
+    </pre>
+    <hr />
+
     <h1 id="link-clicked">Anchor for "link-clicked" test</h1>
 
     <script type="module">
diff --git a/packages/mermaid/src/dagre-wrapper/index.js b/packages/mermaid/src/dagre-wrapper/index.js
index 897f8a7eb1..70f1a862cd 100644
--- a/packages/mermaid/src/dagre-wrapper/index.js
+++ b/packages/mermaid/src/dagre-wrapper/index.js
@@ -54,6 +54,14 @@ const recursiveRender = async (_elem, graph, diagramType, id, parentCluster, sit
       if (node && node.clusterNode) {
         // const children = graph.children(v);
         log.info('Cluster identified', v, node.width, graph.node(v));
+        // `node.graph.setGraph` applies the graph configurations such as nodeSpacing to subgraphs as without this the default values would be used
+        // We override only the `ranksep` and `nodesep` configurations to allow for setting subgraph spacing while avoiding overriding other properties
+        const { ranksep, nodesep } = graph.graph();
+        node.graph.setGraph({
+          ...node.graph.graph(),
+          ranksep,
+          nodesep,
+        });
         const o = await recursiveRender(
           nodes,
           node.graph,