diff --git a/spec/git-repository-spec.coffee b/spec/git-repository-spec.coffee
index ef87d83ee..d427fc3b9 100644
--- a/spec/git-repository-spec.coffee
+++ b/spec/git-repository-spec.coffee
@@ -199,7 +199,7 @@ describe "GitRepository", ->
 
     beforeEach ->
       workingDirectory = copyRepository()
-      repo = new GitRepository(workingDirectory)
+      repo = new GitRepository(workingDirectory, {project: atom.project, config: atom.config})
       modifiedPath = path.join(workingDirectory, 'file.txt')
       newPath = path.join(workingDirectory, 'untracked.txt')
       cleanPath = path.join(workingDirectory, 'other.txt')
@@ -249,6 +249,22 @@ describe "GitRepository", ->
         expect(repo.isStatusModified(status)).toBe false
         expect(repo.isStatusNew(status)).toBe false
 
+    it "works correctly when the project has multiple folders (regression)", ->
+      atom.project.addPath(workingDirectory)
+      atom.project.addPath(path.join(__dirname, 'fixtures', 'dir'))
+      statusHandler = jasmine.createSpy('statusHandler')
+      repo.onDidChangeStatuses statusHandler
+
+      repo.refreshStatus()
+
+      waitsFor ->
+        statusHandler.callCount > 0
+
+      runs ->
+        expect(repo.getCachedPathStatus(cleanPath)).toBeUndefined()
+        expect(repo.isStatusNew(repo.getCachedPathStatus(newPath))).toBeTruthy()
+        expect(repo.isStatusModified(repo.getCachedPathStatus(modifiedPath))).toBeTruthy()
+
     it 'caches statuses that were looked up synchronously', ->
       originalContent = 'undefined'
       fs.writeFileSync(modifiedPath, 'making this path modified')
diff --git a/src/git-repository.coffee b/src/git-repository.coffee
index 85600bba7..c59615378 100644
--- a/src/git-repository.coffee
+++ b/src/git-repository.coffee
@@ -3,6 +3,7 @@
 _ = require 'underscore-plus'
 {Emitter, Disposable, CompositeDisposable} = require 'event-kit'
 fs = require 'fs-plus'
+path = require 'path'
 GitUtils = require 'git-utils'
 
 Task = require './task'
@@ -468,8 +469,8 @@ class GitRepository
     @handlerPath ?= require.resolve('./repository-status-handler')
 
     relativeProjectPaths = @project?.getPaths()
-      .map (path) => @relativize(path)
-      .filter (path) -> path.length > 0
+      .map (projectPath) => @relativize(projectPath)
+      .filter (projectPath) -> projectPath.length > 0 and not path.isAbsolute(projectPath)
 
     @statusTask?.terminate()
     new Promise (resolve) =>