diff --git a/packages/@aws-cdk/core/lib/cfn-resource.ts b/packages/@aws-cdk/core/lib/cfn-resource.ts
index 94ae9c506e5e0..9777268a7b328 100644
--- a/packages/@aws-cdk/core/lib/cfn-resource.ts
+++ b/packages/@aws-cdk/core/lib/cfn-resource.ts
@@ -609,6 +609,35 @@ function deepMerge(target: any, ...sources: any[]) {
           }
         }
 
+        /**
+         * There might also be the case where the source is an intrinsic
+         *
+         *    target: {
+         *      Type: 'MyResourceType',
+         *      Properties: {
+         *        prop1: { subprop: { name: { 'Fn::GetAtt': 'abc' } } }
+         *      }
+         *    }
+         *    sources: [ {
+         *      Properties: {
+         *        prop1: { subprop: { 'Fn::If': ['SomeCondition', {...}, {...}] }}
+         *      }
+         *    } ]
+         *
+         * We end up in a place that is the reverse of the above check, the source
+         * becomes an intrinsic before the target
+         *
+         *   target: { subprop: { name: { 'Fn::GetAtt': 'abc' } } }
+         *   sources: [{
+         *     'Fn::If': [ 'MyCondition', {...}, {...} ]
+         *   }]
+         */
+        if (Object.keys(value).length === 1) {
+          if (MERGE_EXCLUDE_KEYS.includes(Object.keys(value)[0])) {
+            target[key] = {};
+          }
+        }
+
         deepMerge(target[key], value);
 
         // if the result of the merge is an empty object, it's because the
diff --git a/packages/@aws-cdk/core/test/resource.test.ts b/packages/@aws-cdk/core/test/resource.test.ts
index 32a273f76a663..fe247827bb3d6 100644
--- a/packages/@aws-cdk/core/test/resource.test.ts
+++ b/packages/@aws-cdk/core/test/resource.test.ts
@@ -726,6 +726,59 @@ describe('resource', () => {
       });
     });
 
+    test('Can override a an object with an intrinsic', () => {
+      // GIVEN
+      const stack = new Stack();
+
+      const condition = new CfnCondition(stack, 'MyCondition', {
+        expression: Fn.conditionEquals('us-east-1', 'us-east-1'),
+      });
+      const resource = new CfnResource(stack, 'MyResource', {
+        type: 'MyResourceType',
+        properties: {
+          prop1: {
+            subprop: {
+              name: Fn.getAtt('resource', 'abc'),
+            },
+          },
+        },
+      });
+      const isEnabled = Fn.conditionIf(condition.logicalId, {
+        Ref: 'AWS::NoValue',
+      }, {
+        name: Fn.getAtt('resource', 'abc'),
+      });
+
+      // WHEN
+      resource.addPropertyOverride('prop1.subprop', isEnabled);
+      const cfn = toCloudFormation(stack);
+
+      // THEN
+      expect(cfn.Resources.MyResource).toEqual({
+        Type: 'MyResourceType',
+        Properties: {
+          prop1: {
+            subprop: {
+              'Fn::If': [
+                'MyCondition',
+                {
+                  Ref: 'AWS::NoValue',
+                },
+                {
+                  name: {
+                    'Fn::GetAtt': [
+                      'resource',
+                      'abc',
+                    ],
+                  },
+                },
+              ],
+            },
+          },
+        },
+      });
+    });
+
     test('overrides allow overriding a nested intrinsic', () => {
       // GIVEN
       const stack = new Stack();