diff --git a/packages/compiler-cli/ngcc/src/packages/build_marker.ts b/packages/compiler-cli/ngcc/src/packages/build_marker.ts
index 3703183d63..d9b99ff651 100644
--- a/packages/compiler-cli/ngcc/src/packages/build_marker.ts
+++ b/packages/compiler-cli/ngcc/src/packages/build_marker.ts
@@ -59,16 +59,20 @@ export function markAsProcessed(
   }
 
   const scripts = packageJson.scripts || (packageJson.scripts = {});
-  scripts.prepublishOnly__ivy_ngcc_bak =
-      scripts.prepublishOnly__ivy_ngcc_bak || scripts.prepublishOnly;
-
-  scripts.prepublishOnly = 'node --eval \"console.error(\'' +
+  const oldPrepublishOnly = scripts.prepublishOnly;
+  const newPrepublishOnly = 'node --eval \"console.error(\'' +
       'ERROR: Trying to publish a package that has been compiled by NGCC. This is not allowed.\\n' +
       'Please delete and rebuild the package, without compiling with NGCC, before attempting to publish.\\n' +
       'Note that NGCC may have been run by importing this package into another project that is being built with Ivy enabled.\\n' +
       '\')\" ' +
       '&& exit 1';
 
+  if (oldPrepublishOnly && (oldPrepublishOnly !== newPrepublishOnly)) {
+    scripts.prepublishOnly__ivy_ngcc_bak = oldPrepublishOnly;
+  }
+
+  scripts.prepublishOnly = newPrepublishOnly;
+
   // Just in case this package.json was synthesized due to a custom configuration
   // we will ensure that the path to the containing folder exists before we write the file.
   fs.ensureDir(dirname(packageJsonPath));
diff --git a/packages/compiler-cli/ngcc/test/packages/build_marker_spec.ts b/packages/compiler-cli/ngcc/test/packages/build_marker_spec.ts
index 5ce34281aa..1eeb377d1b 100644
--- a/packages/compiler-cli/ngcc/test/packages/build_marker_spec.ts
+++ b/packages/compiler-cli/ngcc/test/packages/build_marker_spec.ts
@@ -147,6 +147,26 @@ runInEachFileSystem(() => {
         expect(pkg.scripts.prepublishOnly).toContain('This is not allowed');
         expect(pkg.scripts.prepublishOnly__ivy_ngcc_bak).toBe(prepublishOnly);
       });
+
+      it(`should not keep backup of overwritten 'prepublishOnly' script`, () => {
+        const COMMON_PACKAGE_PATH = _('/node_modules/@angular/common/package.json');
+        const fs = getFileSystem();
+        let pkg = JSON.parse(fs.readFile(COMMON_PACKAGE_PATH));
+
+        markAsProcessed(fs, pkg, COMMON_PACKAGE_PATH, ['fesm2015']);
+
+        pkg = JSON.parse(fs.readFile(COMMON_PACKAGE_PATH));
+        expect(pkg.scripts.prepublishOnly).toContain('This is not allowed');
+        expect(pkg.scripts.prepublishOnly__ivy_ngcc_bak).toBeUndefined();
+
+        // Running again, now that there is `prepublishOnly` script (created by `ngcc`), it should
+        // still not back it up as `prepublishOnly__ivy_ngcc_bak`.
+        markAsProcessed(fs, pkg, COMMON_PACKAGE_PATH, ['fesm2015']);
+
+        pkg = JSON.parse(fs.readFile(COMMON_PACKAGE_PATH));
+        expect(pkg.scripts.prepublishOnly).toContain('This is not allowed');
+        expect(pkg.scripts.prepublishOnly__ivy_ngcc_bak).toBeUndefined();
+      });
     });
 
     describe('hasBeenProcessed', () => {