diff --git a/spec/package-spec.coffee b/spec/package-spec.coffee
index f8bf4730b..ef5f5a4c3 100644
--- a/spec/package-spec.coffee
+++ b/spec/package-spec.coffee
@@ -7,6 +7,10 @@ describe "Package", ->
   describe "when the package contains incompatible native modules", ->
     beforeEach ->
       spyOn(atom, 'inDevMode').andReturn(false)
+      items = {}
+      spyOn(global.localStorage, 'setItem').andCallFake (key, item) -> items[key] = item; undefined
+      spyOn(global.localStorage, 'getItem').andCallFake (key) -> items[key] ? null
+      spyOn(global.localStorage, 'removeItem').andCallFake (key) -> delete items[key]; undefined
 
     it "does not activate it", ->
       packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-incompatible-native-module')
@@ -17,14 +21,6 @@ describe "Package", ->
 
     it "caches the incompatible native modules in local storage", ->
       packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-incompatible-native-module')
-      cacheKey = null
-      cacheItem = null
-
-      spyOn(global.localStorage, 'setItem').andCallFake (key, item) ->
-        cacheKey = key
-        cacheItem = item
-      spyOn(global.localStorage, 'getItem').andCallFake (key) ->
-        return cacheItem if cacheKey is key
 
       expect(new Package(packagePath).isCompatible()).toBe false
       expect(global.localStorage.getItem.callCount).toBe 1
@@ -35,6 +31,13 @@ describe "Package", ->
       expect(global.localStorage.setItem.callCount).toBe 1
 
   describe "::rebuild()", ->
+    beforeEach ->
+      spyOn(atom, 'inDevMode').andReturn(false)
+      items = {}
+      spyOn(global.localStorage, 'setItem').andCallFake (key, item) -> items[key] = item; undefined
+      spyOn(global.localStorage, 'getItem').andCallFake (key) -> items[key] ? null
+      spyOn(global.localStorage, 'removeItem').andCallFake (key) -> delete items[key]; undefined
+
     it "returns a promise resolving to the results of `apm rebuild`", ->
       packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-index')
       pack = new Package(packagePath)
@@ -52,7 +55,6 @@ describe "Package", ->
     it "persists build failures in local storage", ->
       packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-index')
       pack = new Package(packagePath)
-      global.localStorage.removeItem(pack.getBuildFailureOutputStorageKey())
 
       expect(pack.isCompatible()).toBe true
       expect(pack.getBuildFailureOutput()).toBeNull()
@@ -67,11 +69,31 @@ describe "Package", ->
       expect(pack.getIncompatibleNativeModules()).toEqual []
       expect(pack.isCompatible()).toBe false
 
+      # A different package instance has the same failure output (simulates reload)
       pack2 = new Package(packagePath)
       expect(pack2.getBuildFailureOutput()).toBe 'It is broken'
       expect(pack2.isCompatible()).toBe false
 
-      global.localStorage.removeItem(pack.getBuildFailureOutputStorageKey())
+      # Clears the build failure after a successful build
+      pack.rebuild()
+      rebuildCallbacks[1]({code: 0, stdout: 'It worked'})
+
+      expect(pack.getBuildFailureOutput()).toBeNull()
+      expect(pack2.getBuildFailureOutput()).toBeNull()
+
+    it "sets cached incompatible modules to an empty array when the rebuild completes (there may be a build error, but rebuilding *deletes* native modules)", ->
+      packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-incompatible-native-module')
+      pack = new Package(packagePath)
+
+      expect(pack.getIncompatibleNativeModules().length).toBeGreaterThan(0)
+
+      rebuildCallbacks = []
+      spyOn(pack, 'runRebuildProcess').andCallFake ((callback) -> rebuildCallbacks.push(callback))
+
+      pack.rebuild()
+      expect(pack.getIncompatibleNativeModules().length).toBeGreaterThan(0)
+      rebuildCallbacks[0]({code: 0, stdout: 'It worked'})
+      expect(pack.getIncompatibleNativeModules().length).toBe(0)
 
   describe "theme", ->
     theme = null
diff --git a/src/package.coffee b/src/package.coffee
index 467204428..db6c77533 100644
--- a/src/package.coffee
+++ b/src/package.coffee
@@ -635,9 +635,12 @@ class Package
   rebuild: ->
     new Promise (resolve) =>
       @runRebuildProcess (result) =>
-        if result.code isnt 0
+        if result.code is 0
+          global.localStorage.removeItem(@getBuildFailureOutputStorageKey())
+        else
           @compatible = false
           global.localStorage.setItem(@getBuildFailureOutputStorageKey(), result.stderr)
+        global.localStorage.setItem(@getIncompatibleNativeModulesStorageKey(), '[]')
         resolve(result)
 
   # Extended: If a previous rebuild failed, get the contents of stderr.
@@ -661,6 +664,9 @@ class Package
   getBuildFailureOutputStorageKey: ->
     "installed-packages:#{@name}:#{@metadata.version}:build-error"
 
+  getIncompatibleNativeModulesStorageKey: ->
+    "installed-packages:#{@name}:#{@metadata.version}:incompatible-native-modules"
+
   # Get the incompatible native modules that this package depends on.
   # This recurses through all dependencies and requires all modules that
   # contain a `.node` file.
@@ -668,11 +674,10 @@ class Package
   # This information is cached in local storage on a per package/version basis
   # to minimize the impact on startup time.
   getIncompatibleNativeModules: ->
-    localStorageKey = "installed-packages:#{@name}:#{@metadata.version}"
     unless atom.inDevMode()
       try
-        {incompatibleNativeModules} = JSON.parse(global.localStorage.getItem(localStorageKey)) ? {}
-      return incompatibleNativeModules if incompatibleNativeModules?
+        if arrayAsString = global.localStorage.getItem(@getIncompatibleNativeModulesStorageKey())
+          return JSON.parse(arrayAsString)
 
     incompatibleNativeModules = []
     for nativeModulePath in @getNativeModuleDependencyPaths()
@@ -687,7 +692,7 @@ class Package
           version: version
           error: error.message
 
-    global.localStorage.setItem(localStorageKey, JSON.stringify({incompatibleNativeModules}))
+    global.localStorage.setItem(@getIncompatibleNativeModulesStorageKey(), JSON.stringify(incompatibleNativeModules))
     incompatibleNativeModules
 
   handleError: (message, error) ->