diff --git a/spec/fixtures/packages/package-with-cached-incompatible-native-module/main.js b/spec/fixtures/packages/package-with-cached-incompatible-native-module/main.js
new file mode 100644
index 000000000..e69de29bb
diff --git a/spec/fixtures/packages/package-with-cached-incompatible-native-module/package.json b/spec/fixtures/packages/package-with-cached-incompatible-native-module/package.json
new file mode 100644
index 000000000..1db0a0a9d
--- /dev/null
+++ b/spec/fixtures/packages/package-with-cached-incompatible-native-module/package.json
@@ -0,0 +1,12 @@
+{
+  "name": "package-with-cached-incompatible-native-module",
+  "version": "1.0.0",
+  "main": "./main.js",
+  "_atomModuleCache": {
+    "extensions": {
+      ".node": [
+        "node_modules/native-module/build/Release/native.node"
+      ]
+    }
+  }
+}
diff --git a/spec/fixtures/packages/package-with-ignored-incompatible-native-module/package.json b/spec/fixtures/packages/package-with-ignored-incompatible-native-module/package.json
index 70de63b9d..4f6206828 100644
--- a/spec/fixtures/packages/package-with-ignored-incompatible-native-module/package.json
+++ b/spec/fixtures/packages/package-with-ignored-incompatible-native-module/package.json
@@ -1,5 +1,5 @@
 {
-  "name": "package-with-incompatible-native-module-and-atom-module-cache",
+  "name": "package-with-ignored-incompatible-native-module",
   "version": "1.0.0",
   "main": "./main.js",
   "_atomModuleCache": {
diff --git a/spec/package-spec.coffee b/spec/package-spec.coffee
index 8f7f2c0bf..e73782219 100644
--- a/spec/package-spec.coffee
+++ b/spec/package-spec.coffee
@@ -19,13 +19,16 @@ describe "Package", ->
       expect(pack.incompatibleModules[0].name).toBe 'native-module'
       expect(pack.incompatibleModules[0].path).toBe path.join(packagePath, 'node_modules', 'native-module')
 
-    it "utilizes _atomModuleCache to get native modules and skips traversing through submodules", ->
+    it "utilizes _atomModuleCache if present to determine the package's native dependencies", ->
       packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-ignored-incompatible-native-module')
       pack = new Package(packagePath)
-      # Since `_atomModuleCache` exists and it doesn't have the record of the
-      # incompatible native module, this package is recognized as compatible.
+      expect(pack.getNativeModuleDependencyPaths().length).toBe(1) # doesn't see the incompatible module
       expect(pack.isCompatible()).toBe true
 
+      packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-cached-incompatible-native-module')
+      pack = new Package(packagePath)
+      expect(pack.isCompatible()).toBe false
+
     it "caches the incompatible native modules in local storage", ->
       packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-incompatible-native-module')
 
diff --git a/src/package.coffee b/src/package.coffee
index c38ea08f7..6170a645e 100644
--- a/src/package.coffee
+++ b/src/package.coffee
@@ -598,11 +598,10 @@ class Package
     nativeModulePaths = []
 
     if @metadata._atomModuleCache?
-      nativeModuleBindingPaths = @metadata._atomModuleCache.extensions?['.node'] ? []
-      for nativeModuleBindingPath in nativeModuleBindingPaths
-        # The `.node` file lies in nativeModulePath/build/Release/ folder.
-        nativeModulePath = path.join(path.dirname(nativeModuleBindingPath), '..', '..')
-        nativeModulePaths.push(nativeModulePath) if @isNativeModule(nativeModulePath)
+      relativeNativeModuleBindingPaths = @metadata._atomModuleCache.extensions?['.node'] ? []
+      for relativeNativeModuleBindingPath in relativeNativeModuleBindingPaths
+        nativeModulePath = path.join(@path, relativeNativeModuleBindingPath, '..', '..', '..')
+        nativeModulePaths.push(nativeModulePath)
       return nativeModulePaths
 
     traversePath = (nodeModulesPath) =>