diff --git a/spec/atom-environment-spec.coffee b/spec/atom-environment-spec.coffee
index 3283b63d6..6271ea5d4 100644
--- a/spec/atom-environment-spec.coffee
+++ b/spec/atom-environment-spec.coffee
@@ -362,3 +362,16 @@ describe "AtomEnvironment", ->
 
       version = '1.7.0-dev-5340c91'
       expect(atom.getReleaseChannel()).toBe 'dev'
+
+  describe "environment patching", ->
+    it "patches process.env on startup", ->
+      configDirPath = temp.mkdirSync()
+      fakeDocument = {
+        addEventListener: ->
+        removeEventListener: ->
+        head: document.createElement('head')
+        body: document.createElement('body')
+      }
+      atomEnvironment = new AtomEnvironment({applicationDelegate: atom.applicationDelegate, window, document: fakeDocument})
+
+      expect(process.env).toEqual atomEnvironment.project.getEnv()
diff --git a/src/atom-environment.coffee b/src/atom-environment.coffee
index 8c79d66f6..d1e921d54 100644
--- a/src/atom-environment.coffee
+++ b/src/atom-environment.coffee
@@ -230,6 +230,10 @@ class AtomEnvironment extends Model
 
     checkPortableHomeWritable()
 
+    # Patch the `process.env` on startup to fix the problem first documented
+    # in #4126
+    process.env = @project.getEnv()
+
   attachSaveStateListeners: ->
     saveState = => @saveState({isUnloading: false}) unless @unloaded
     debouncedSaveState = _.debounce(saveState, @saveStateDebounceInterval)