diff --git a/spec-nylas/stores/unread-count-store-spec.coffee b/spec-nylas/stores/unread-count-store-spec.coffee
new file mode 100644
index 000000000..caf7a2e91
--- /dev/null
+++ b/spec-nylas/stores/unread-count-store-spec.coffee
@@ -0,0 +1,75 @@
+UnreadCountStore = require '../../src/flux/stores/unread-count-store'
+NamespaceStore = require '../../src/flux/stores/namespace-store'
+DatabaseStore = require '../../src/flux/stores/database-store'
+Folder = require '../../src/flux/models/folder'
+Label = require '../../src/flux/models/label'
+Thread = require '../../src/flux/models/thread'
+Category = require '../../src/flux/models/category'
+
+describe "UnreadCountStore", ->
+  describe "_fetchCount", ->
+    beforeEach ->
+      atom.testOrganizationUnit = 'folder'
+      spyOn(DatabaseStore, 'findBy').andCallFake =>
+        Promise.resolve(new Category({id: 'inbox-category-id'}))
+      spyOn(DatabaseStore, 'count').andCallFake =>
+        Promise.resolve(100)
+
+    it "should create the correct query when using folders", ->
+      atom.testOrganizationUnit = 'folder'
+      UnreadCountStore._fetchCount()
+      advanceClock()
+      expect(DatabaseStore.findBy).toHaveBeenCalledWith(Folder, {name: 'inbox'})
+
+      [Model, Matchers] = DatabaseStore.count.calls[0].args
+      expect(Model).toBe(Thread)
+      expect(Matchers[0].attr.modelKey).toBe('namespaceId')
+      expect(Matchers[1].attr.modelKey).toBe('unread')
+      expect(Matchers[1].val).toBe(true)
+      expect(Matchers[2].attr.modelKey).toBe('folders')
+      expect(Matchers[2].val).toBe('inbox-category-id')
+
+    it "should create the correct query when using labels", ->
+      atom.testOrganizationUnit = 'label'
+      UnreadCountStore._fetchCount()
+      advanceClock()
+      expect(DatabaseStore.findBy).toHaveBeenCalledWith(Label, {name: 'inbox'})
+
+      [Model, Matchers] = DatabaseStore.count.calls[0].args
+      expect(Matchers[0].attr.modelKey).toBe('namespaceId')
+      expect(Matchers[1].attr.modelKey).toBe('unread')
+      expect(Matchers[1].val).toBe(true)
+      expect(Matchers[2].attr.modelKey).toBe('labels')
+      expect(Matchers[2].val).toBe('inbox-category-id')
+
+    it "should not trigger if the unread count is the same", ->
+      spyOn(UnreadCountStore, 'trigger')
+      UnreadCountStore._count = 100
+      UnreadCountStore._fetchCount()
+      advanceClock()
+      expect(UnreadCountStore.trigger).not.toHaveBeenCalled()
+
+      UnreadCountStore._count = 101
+      UnreadCountStore._fetchCount()
+      advanceClock()
+      expect(UnreadCountStore.trigger).toHaveBeenCalled()
+
+    it "should update the badge count", ->
+      UnreadCountStore._count = 101
+      spyOn(UnreadCountStore, '_updateBadgeForCount')
+      UnreadCountStore._fetchCount()
+      advanceClock()
+      expect(UnreadCountStore._updateBadgeForCount).toHaveBeenCalled()
+
+  describe "_updateBadgeForCount", ->
+    it "should set the badge correctly", ->
+      spyOn(UnreadCountStore, '_setBadge')
+      spyOn(atom, 'isMainWindow').andCallFake -> true
+      UnreadCountStore._updateBadgeForCount(0)
+      expect(UnreadCountStore._setBadge).toHaveBeenCalledWith("")
+      UnreadCountStore._updateBadgeForCount(1)
+      expect(UnreadCountStore._setBadge).toHaveBeenCalledWith("1")
+      UnreadCountStore._updateBadgeForCount(100)
+      expect(UnreadCountStore._setBadge).toHaveBeenCalledWith("100")
+      UnreadCountStore._updateBadgeForCount(1000)
+      expect(UnreadCountStore._setBadge).toHaveBeenCalledWith("999+")
diff --git a/src/flux/stores/unread-count-store.coffee b/src/flux/stores/unread-count-store.coffee
index af1be3e98..0404a66e0 100644
--- a/src/flux/stores/unread-count-store.coffee
+++ b/src/flux/stores/unread-count-store.coffee
@@ -2,10 +2,13 @@ Reflux = require 'reflux'
 _ = require 'underscore'
 remote = require 'remote'
 app = remote.require 'app'
+CategoryStore = require './category-store'
 NamespaceStore = require './namespace-store'
 DatabaseStore = require './database-store'
 Actions = require '../actions'
 Thread = require '../models/thread'
+Folder = require '../models/folder'
+Label = require '../models/label'
 
 ###
 Public: The UnreadCountStore exposes a simple API for getting the number of
@@ -39,24 +42,31 @@ UnreadCountStore = Reflux.createStore
     namespace = NamespaceStore.current()
     return unless namespace
 
-    matchers = [
-      Thread.attributes.namespaceId.equal(namespace.id),
-      Thread.attributes.unread.equal(true),
-    ]
     if namespace.usesFolders()
-      matchers.push(Thread.attributes.folders.contains('inbox'))
+      [CategoryClass, CategoryAttribute] = [Folder, Thread.attributes.folders]
     else if namespace.usesLabels()
-      matchers.push(Thread.attributes.labels.contains('inbox'))
+      [CategoryClass, CategoryAttribute] = [Label, Thread.attributes.labels]
     else
       return
 
-    DatabaseStore.count(Thread, matchers).then (count) =>
-      return if @_count is count
-      @_count = count
-      @_updateBadgeForCount(count)
-      @trigger()
-    .catch (err) =>
-      console.warn("Failed to fetch unread count: #{err}")
+    # Note: We can't use the convenience methods on CategoryStore to fetch the
+    # category because it may not have been loaded yet
+    DatabaseStore.findBy(CategoryClass, {name: 'inbox'}).then (category) =>
+      return unless category
+
+      matchers = [
+        Thread.attributes.namespaceId.equal(namespace.id),
+        Thread.attributes.unread.equal(true),
+        CategoryAttribute.contains(category.id)
+      ]
+
+      DatabaseStore.count(Thread, matchers).then (count) =>
+        return if @_count is count
+        @_count = count
+        @_updateBadgeForCount(count)
+        @trigger()
+      .catch (err) =>
+        console.warn("Failed to fetch unread count: #{err}")
 
   _updateBadgeForCount: (count) ->
     return unless atom.isMainWindow()