diff --git a/benchmarks/benchmark-runner.js b/benchmarks/benchmark-runner.js
index 30b23ffbf..56a37cfd4 100644
--- a/benchmarks/benchmark-runner.js
+++ b/benchmarks/benchmark-runner.js
@@ -65,7 +65,7 @@ export default async function ({test, benchmarkPaths}) {
         console.log(textualOutput)
       }
 
-      global.atom.reset()
+      await global.atom.reset()
     }
   }
 
diff --git a/spec/grammars-spec.coffee b/spec/grammars-spec.coffee
index 7d4754397..7b70797ba 100644
--- a/spec/grammars-spec.coffee
+++ b/spec/grammars-spec.coffee
@@ -22,10 +22,12 @@ describe "the `grammars` global", ->
       atom.packages.activatePackage('language-git')
 
   afterEach ->
-    atom.packages.deactivatePackages()
-    atom.packages.unloadPackages()
-    try
-      temp.cleanupSync()
+    waitsForPromise ->
+      atom.packages.deactivatePackages()
+    runs ->
+      atom.packages.unloadPackages()
+      try
+        temp.cleanupSync()
 
   describe ".selectGrammar(filePath)", ->
     it "always returns a grammar", ->
diff --git a/spec/language-mode-spec.coffee b/spec/language-mode-spec.coffee
index 4025472af..aca96d2cc 100644
--- a/spec/language-mode-spec.coffee
+++ b/spec/language-mode-spec.coffee
@@ -15,8 +15,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-javascript')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe ".minIndentLevelForRowRange(startRow, endRow)", ->
       it "returns the minimum indent level for the given row range", ->
@@ -175,8 +177,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-coffee-script')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe ".toggleLineCommentsForBufferRows(start, end)", ->
       it "comments/uncomments lines in the given range", ->
@@ -222,8 +226,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-css')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe ".toggleLineCommentsForBufferRows(start, end)", ->
       it "comments/uncomments lines in the given range", ->
@@ -274,8 +280,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-css')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe "when commenting lines", ->
       it "only uses the `commentEnd` pattern if it comes from the same grammar as the `commentStart`", ->
@@ -294,8 +302,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-xml')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe "when uncommenting lines", ->
       it "removes the leading whitespace from the comment end pattern match", ->
@@ -313,8 +323,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-javascript')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     it "maintains cursor buffer position when a folding/unfolding", ->
       editor.setCursorBufferPosition([5, 5])
@@ -403,8 +415,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-javascript')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe ".unfoldAll()", ->
       it "unfolds every folded line", ->
@@ -481,8 +495,10 @@ describe "LanguageMode", ->
         atom.packages.activatePackage('language-css')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     describe "suggestedIndentForBufferRow", ->
       it "does not return negative values (regression)", ->
diff --git a/spec/package-manager-spec.coffee b/spec/package-manager-spec.coffee
index 88efff4ae..9b7d46340 100644
--- a/spec/package-manager-spec.coffee
+++ b/spec/package-manager-spec.coffee
@@ -56,8 +56,10 @@ describe "PackageManager", ->
       spyOn(atom.packages, 'loadAvailablePackage')
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
 
     it "sets hasLoadedInitialPackages", ->
       expect(atom.packages.hasLoadedInitialPackages()).toBe false
@@ -172,8 +174,10 @@ describe "PackageManager", ->
       model2 = {worksWithViewProvider2: true}
 
       afterEach ->
-        atom.packages.deactivatePackage('package-with-view-providers')
-        atom.packages.unloadPackage('package-with-view-providers')
+        waitsForPromise ->
+          atom.packages.deactivatePackage('package-with-view-providers')
+        runs ->
+          atom.packages.unloadPackage('package-with-view-providers')
 
       it "does not load the view providers immediately", ->
         pack = atom.packages.loadPackage("package-with-view-providers")
@@ -641,7 +645,11 @@ describe "PackageManager", ->
 
         runs ->
           expect(mainModule.activate.callCount).toBe 1
+
+        waitsForPromise ->
           atom.packages.deactivatePackage('package-with-activation-hooks')
+
+        runs ->
           promise = atom.packages.activatePackage('package-with-activation-hooks')
           atom.packages.triggerActivationHook('language-fictitious:grammar-used')
           atom.packages.triggerDeferredActivationHooks()
@@ -704,7 +712,9 @@ describe "PackageManager", ->
         expect(pack.mainModule.someNumber).not.toBe 77
         pack.mainModule.someNumber = 77
         atom.packages.serializePackage("package-with-serialization")
+      waitsForPromise ->
         atom.packages.deactivatePackage("package-with-serialization")
+      runs ->
         spyOn(pack.mainModule, 'activate').andCallThrough()
       waitsForPromise ->
         atom.packages.activatePackage("package-with-serialization")
@@ -872,6 +882,7 @@ describe "PackageManager", ->
             expect(events.length).toBe(1)
             expect(events[0].type).toBe("user-command")
 
+          waitsForPromise ->
             atom.packages.deactivatePackage("package-with-keymaps")
 
           waitsForPromise ->
@@ -1041,12 +1052,15 @@ describe "PackageManager", ->
           consumerModule.consumeFirstServiceV4.reset()
           consumerModule.consumeSecondService.reset()
 
+        waitsForPromise ->
           atom.packages.deactivatePackage("package-with-provided-services")
 
+        runs ->
           expect(firstServiceV3Disposed).toBe true
           expect(firstServiceV4Disposed).toBe true
           expect(secondServiceDisposed).toBe true
 
+        waitsForPromise ->
           atom.packages.deactivatePackage("package-with-consumed-services")
 
         waitsForPromise ->
@@ -1112,8 +1126,11 @@ describe "PackageManager", ->
       runs ->
         spyOn(pack1.mainModule, 'deactivate')
         spyOn(pack2.mainModule, 'serialize')
+
+      waitsForPromise ->
         atom.packages.deactivatePackages()
 
+      runs ->
         expect(pack1.mainModule.deactivate).toHaveBeenCalled()
         expect(pack2.mainModule.serialize).not.toHaveBeenCalled()
 
@@ -1131,7 +1148,10 @@ describe "PackageManager", ->
         expect(atom.packages.isPackageActive("package-with-deactivate")).toBeTruthy()
         spyOn(pack.mainModule, 'deactivate').andCallThrough()
 
+      waitsForPromise ->
         atom.packages.deactivatePackage("package-with-deactivate")
+
+      runs ->
         expect(pack.mainModule.deactivate).toHaveBeenCalled()
         expect(atom.packages.isPackageActive("package-with-module")).toBeFalsy()
 
@@ -1145,26 +1165,38 @@ describe "PackageManager", ->
         expect(atom.packages.isPackageActive("package-that-throws-on-activate")).toBeTruthy()
         spyOn(badPack.mainModule, 'deactivate').andCallThrough()
 
+      waitsForPromise ->
         atom.packages.deactivatePackage("package-that-throws-on-activate")
+
+      runs ->
         expect(badPack.mainModule.deactivate).not.toHaveBeenCalled()
         expect(atom.packages.isPackageActive("package-that-throws-on-activate")).toBeFalsy()
 
     it "absorbs exceptions that are thrown by the package module's deactivate method", ->
       spyOn(console, 'error')
+      thrownError = null
 
       waitsForPromise ->
         atom.packages.activatePackage("package-that-throws-on-deactivate")
 
+      waitsForPromise ->
+        try
+          atom.packages.deactivatePackage("package-that-throws-on-deactivate")
+        catch error
+          thrownError = error
+
       runs ->
-        expect(-> atom.packages.deactivatePackage("package-that-throws-on-deactivate")).not.toThrow()
+        expect(thrownError).toBeNull()
         expect(console.error).toHaveBeenCalled()
 
     it "removes the package's grammars", ->
       waitsForPromise ->
         atom.packages.activatePackage('package-with-grammars')
 
-      runs ->
+      waitsForPromise ->
         atom.packages.deactivatePackage('package-with-grammars')
+
+      runs ->
         expect(atom.grammars.selectGrammar('a.alot').name).toBe 'Null Grammar'
         expect(atom.grammars.selectGrammar('a.alittle').name).toBe 'Null Grammar'
 
@@ -1172,8 +1204,10 @@ describe "PackageManager", ->
       waitsForPromise ->
         atom.packages.activatePackage('package-with-keymaps')
 
-      runs ->
+      waitsForPromise ->
         atom.packages.deactivatePackage('package-with-keymaps')
+
+      runs ->
         expect(atom.keymaps.findKeyBindings(keystrokes: 'ctrl-z', target: createTestElement('test-1'))).toHaveLength 0
         expect(atom.keymaps.findKeyBindings(keystrokes: 'ctrl-z', target: createTestElement('test-2'))).toHaveLength 0
 
@@ -1181,8 +1215,10 @@ describe "PackageManager", ->
       waitsForPromise ->
         atom.packages.activatePackage('package-with-styles')
 
-      runs ->
+      waitsForPromise ->
         atom.packages.deactivatePackage('package-with-styles')
+
+      runs ->
         one = require.resolve("./fixtures/packages/package-with-style-sheets-manifest/styles/1.css")
         two = require.resolve("./fixtures/packages/package-with-style-sheets-manifest/styles/2.less")
         three = require.resolve("./fixtures/packages/package-with-style-sheets-manifest/styles/3.css")
@@ -1196,17 +1232,26 @@ describe "PackageManager", ->
 
       runs ->
         expect(atom.config.get 'editor.increaseIndentPattern', scope: ['.source.omg']).toBe '^a'
+
+      waitsForPromise ->
         atom.packages.deactivatePackage("package-with-settings")
+
+      runs ->
         expect(atom.config.get 'editor.increaseIndentPattern', scope: ['.source.omg']).toBeUndefined()
 
     it "invokes ::onDidDeactivatePackage listeners with the deactivated package", ->
+      deactivatedPackage = null
+
       waitsForPromise ->
         atom.packages.activatePackage("package-with-main")
 
       runs ->
-        deactivatedPackage = null
         atom.packages.onDidDeactivatePackage (pack) -> deactivatedPackage = pack
+
+      waitsForPromise ->
         atom.packages.deactivatePackage("package-with-main")
+
+      runs ->
         expect(deactivatedPackage.name).toBe "package-with-main"
 
   describe "::activate()", ->
@@ -1220,10 +1265,11 @@ describe "PackageManager", ->
       expect(loadedPackages.length).toBeGreaterThan 0
 
     afterEach ->
-      atom.packages.deactivatePackages()
-      atom.packages.unloadPackages()
-
-      jasmine.restoreDeprecationsSnapshot()
+      waitsForPromise ->
+        atom.packages.deactivatePackages()
+      runs ->
+        atom.packages.unloadPackages()
+        jasmine.restoreDeprecationsSnapshot()
 
     it "sets hasActivatedInitialPackages", ->
       spyOn(atom.styles, 'getUserStyleSheetPath').andReturn(null)
@@ -1286,6 +1332,9 @@ describe "PackageManager", ->
 
       it "disables an enabled package", ->
         packageName = 'package-with-main'
+        pack = null
+        activatedPackages = null
+
         waitsForPromise ->
           atom.packages.activatePackage(packageName)
 
@@ -1295,7 +1344,11 @@ describe "PackageManager", ->
 
           pack = atom.packages.disablePackage(packageName)
 
+        waitsFor ->
           activatedPackages = atom.packages.getActivePackages()
+          activatedPackages.length is 0
+
+        runs ->
           expect(activatedPackages).not.toContain(pack)
           expect(atom.config.get('core.disabledPackages')).toContain packageName
 
@@ -1322,7 +1375,8 @@ describe "PackageManager", ->
           atom.themes.activateThemes()
 
       afterEach ->
-        atom.themes.deactivateThemes()
+        waitsForPromise ->
+          atom.themes.deactivateThemes()
 
       it "enables and disables a theme", ->
         packageName = 'theme-with-package-file'
diff --git a/spec/package-spec.coffee b/spec/package-spec.coffee
index 5018d2eb4..e7bfd0249 100644
--- a/spec/package-spec.coffee
+++ b/spec/package-spec.coffee
@@ -138,7 +138,8 @@ describe "Package", ->
       jasmine.attachToDOM(editorElement)
 
     afterEach ->
-      theme.deactivate() if theme?
+      waitsForPromise ->
+        Promise.resolve(theme.deactivate()) if theme?
 
     describe "when the theme contains a single style file", ->
       it "loads and applies css", ->
@@ -200,8 +201,10 @@ describe "Package", ->
 
       it "deactivated event fires on .deactivate()", ->
         theme.onDidDeactivate spy = jasmine.createSpy()
-        theme.deactivate()
-        expect(spy).toHaveBeenCalled()
+        waitsForPromise ->
+          Promise.resolve(theme.deactivate())
+        runs ->
+          expect(spy).toHaveBeenCalled()
 
   describe ".loadMetadata()", ->
     [packagePath, metadata] = []
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index eec8ce5fb..c20bfc827 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -108,10 +108,14 @@ beforeEach ->
 afterEach ->
   ensureNoDeprecatedFunctionCalls()
   ensureNoDeprecatedStylesheets()
-  atom.reset()
-  document.getElementById('jasmine-content').innerHTML = '' unless window.debugContent
-  warnIfLeakingPathSubscriptions()
-  waits(0) # yield to ui thread to make screen update more frequently
+
+  waitsForPromise ->
+    atom.reset()
+
+  runs ->
+    document.getElementById('jasmine-content').innerHTML = '' unless window.debugContent
+    warnIfLeakingPathSubscriptions()
+    waits(0) # yield to ui thread to make screen update more frequently
 
 warnIfLeakingPathSubscriptions = ->
   watchedPaths = pathwatcher.getWatchedPaths()
diff --git a/spec/text-editor-registry-spec.js b/spec/text-editor-registry-spec.js
index 79d575a5f..2479bff9b 100644
--- a/spec/text-editor-registry-spec.js
+++ b/spec/text-editor-registry-spec.js
@@ -685,7 +685,7 @@ describe('TextEditorRegistry', function () {
       registry.setGrammarOverride(editor, 'source.c')
       registry.setGrammarOverride(editor2, 'source.js')
 
-      atom.packages.deactivatePackage('language-javascript')
+      await atom.packages.deactivatePackage('language-javascript')
 
       const editorCopy = TextEditor.deserialize(editor.serialize(), atom)
       const editor2Copy = TextEditor.deserialize(editor2.serialize(), atom)
diff --git a/spec/theme-manager-spec.coffee b/spec/theme-manager-spec.coffee
index 5d2912f5b..86237b71d 100644
--- a/spec/theme-manager-spec.coffee
+++ b/spec/theme-manager-spec.coffee
@@ -8,9 +8,11 @@ describe "atom.themes", ->
     spyOn(console, 'warn')
 
   afterEach ->
-    atom.themes.deactivateThemes()
-    try
-      temp.cleanupSync()
+    waitsForPromise ->
+      atom.themes.deactivateThemes()
+    runs ->
+      try
+        temp.cleanupSync()
 
   describe "theme getters and setters", ->
     beforeEach ->
diff --git a/src/atom-environment.coffee b/src/atom-environment.coffee
index b37acddd1..bd631435e 100644
--- a/src/atom-environment.coffee
+++ b/src/atom-environment.coffee
@@ -328,20 +328,14 @@ class AtomEnvironment extends Model
 
     @contextMenu.clear()
 
-    @packages.reset()
-
-    @workspace.reset(@packages)
-    @registerDefaultOpeners()
-
-    @project.reset(@packages)
-
-    @workspace.subscribeToEvents()
-
-    @grammars.clear()
-
-    @textEditors.clear()
-
-    @views.clear()
+    @packages.reset().then =>
+      @workspace.reset(@packages)
+      @registerDefaultOpeners()
+      @project.reset(@packages)
+      @workspace.subscribeToEvents()
+      @grammars.clear()
+      @textEditors.clear()
+      @views.clear()
 
   destroy: ->
     return if not @project
@@ -702,6 +696,11 @@ class AtomEnvironment extends Model
                 windowCloseRequested: true,
                 projectHasPaths: @project.getPaths().length > 0
               })
+            .then (closing) =>
+              if closing
+                @packages.deactivatePackages().then -> closing
+              else
+                closing
 
         @listenForUpdates()
 
@@ -758,7 +757,6 @@ class AtomEnvironment extends Model
     return if not @project
 
     @storeWindowBackground()
-    @packages.deactivatePackages()
     @saveBlobStoreSync()
     @unloaded = true
 
diff --git a/src/package-manager.js b/src/package-manager.js
index 73855ae37..b52e29cad 100644
--- a/src/package-manager.js
+++ b/src/package-manager.js
@@ -77,9 +77,9 @@ module.exports = class PackageManager {
     this.themeManager = themeManager
   }
 
-  reset () {
+  async reset () {
     this.serviceHub.clear()
-    this.deactivatePackages()
+    await this.deactivatePackages()
     this.loadedPackages = {}
     this.preloadedPackages = {}
     this.packageStates = {}
@@ -744,21 +744,30 @@ module.exports = class PackageManager {
   }
 
   // Deactivate all packages
-  deactivatePackages () {
-    this.config.transact(() => {
-      this.getLoadedPackages().forEach(pack => this.deactivatePackage(pack.name, true))
-    })
+  async deactivatePackages () {
+    await this.config.transactAsync(() =>
+      Promise.all(this.getLoadedPackages().map(pack => this.deactivatePackage(pack.name, true)))
+    )
     this.unobserveDisabledPackages()
     this.unobservePackagesWithKeymapsDisabled()
   }
 
   // Deactivate the package with the given name
-  deactivatePackage (name, suppressSerialization) {
+  async deactivatePackage (name, suppressSerialization) {
     const pack = this.getLoadedPackage(name)
+    if (pack == null) {
+      return
+    }
+
     if (!suppressSerialization && this.isPackageActive(pack.name)) {
       this.serializePackage(pack)
     }
-    pack.deactivate()
+
+    const deactivationResult = pack.deactivate()
+    if (deactivationResult && typeof deactivationResult.then === 'function') {
+      await deactivationResult
+    }
+
     delete this.activePackages[pack.name]
     delete this.activatingPackages[pack.name]
     this.emitter.emit('did-deactivate-package', pack)
diff --git a/src/package.coffee b/src/package.coffee
index 039ccf9d3..fdd89bc74 100644
--- a/src/package.coffee
+++ b/src/package.coffee
@@ -506,14 +506,29 @@ class Package
     @configSchemaRegisteredOnActivate = false
     @deactivateResources()
     @deactivateKeymaps()
-    if @mainActivated
-      try
-        @mainModule?.deactivate?()
-        @mainModule?.deactivateConfig?()
-        @mainActivated = false
-        @mainInitialized = false
-      catch e
-        console.error "Error deactivating package '#{@name}'", e.stack
+
+    unless @mainActivated
+      @emitter.emit 'did-deactivate'
+      return
+
+    try
+      deactivationResult = @mainModule?.deactivate?()
+    catch e
+      console.error "Error deactivating package '#{@name}'", e.stack
+
+    # We support then-able async promises as well as sync ones from deactivate
+    if deactivationResult?.then is 'function'
+      deactivationResult.then => @afterDeactivation()
+    else
+      @afterDeactivation()
+
+  afterDeactivation: ->
+    try
+      @mainModule?.deactivateConfig?()
+    catch e
+      console.error "Error deactivating package '#{@name}'", e.stack
+    @mainActivated = false
+    @mainInitialized = false
     @emitter.emit 'did-deactivate'
 
   deactivateResources: ->
diff --git a/src/theme-manager.coffee b/src/theme-manager.coffee
index 0f019dbf0..d6a67ee61 100644
--- a/src/theme-manager.coffee
+++ b/src/theme-manager.coffee
@@ -262,33 +262,31 @@ class ThemeManager
     new Promise (resolve) =>
       # @config.observe runs the callback once, then on subsequent changes.
       @config.observe 'core.themes', =>
-        @deactivateThemes()
+        @deactivateThemes().then =>
+          @warnForNonExistentThemes()
+          @refreshLessCache() # Update cache for packages in core.themes config
 
-        @warnForNonExistentThemes()
+          promises = []
+          for themeName in @getEnabledThemeNames()
+            if @packageManager.resolvePackagePath(themeName)
+              promises.push(@packageManager.activatePackage(themeName))
+            else
+              console.warn("Failed to activate theme '#{themeName}' because it isn't installed.")
 
-        @refreshLessCache() # Update cache for packages in core.themes config
-
-        promises = []
-        for themeName in @getEnabledThemeNames()
-          if @packageManager.resolvePackagePath(themeName)
-            promises.push(@packageManager.activatePackage(themeName))
-          else
-            console.warn("Failed to activate theme '#{themeName}' because it isn't installed.")
-
-        Promise.all(promises).then =>
-          @addActiveThemeClasses()
-          @refreshLessCache() # Update cache again now that @getActiveThemes() is populated
-          @loadUserStylesheet()
-          @reloadBaseStylesheets()
-          @initialLoadComplete = true
-          @emitter.emit 'did-change-active-themes'
-          resolve()
+          Promise.all(promises).then =>
+            @addActiveThemeClasses()
+            @refreshLessCache() # Update cache again now that @getActiveThemes() is populated
+            @loadUserStylesheet()
+            @reloadBaseStylesheets()
+            @initialLoadComplete = true
+            @emitter.emit 'did-change-active-themes'
+            resolve()
 
   deactivateThemes: ->
     @removeActiveThemeClasses()
     @unwatchUserStylesheet()
-    @packageManager.deactivatePackage(pack.name) for pack in @getActiveThemes()
-    null
+    results = @getActiveThemes().map((pack) => @packageManager.deactivatePackage(pack.name))
+    Promise.all(results.filter((r) -> typeof r?.then is 'function'))
 
   isInitialLoadComplete: -> @initialLoadComplete