diff --git a/src/beautifiers/autopep8.coffee b/src/beautifiers/autopep8.coffee
index cc1a234..e38a648 100644
--- a/src/beautifiers/autopep8.coffee
+++ b/src/beautifiers/autopep8.coffee
@@ -27,8 +27,12 @@ module.exports = class Autopep8 extends Beautifier
       })
       .then(=>
         if options.sort_imports
+          editor = atom.workspace.getActiveTextEditor()
+          filePath = editor.getPath()
+          projectPath = atom.project.relativizePath(filePath)[0]
+
           @run("isort",
-            [tempFile],
+            ["-sp", projectPath, tempFile],
             help: {
               link: "https://github.com/timothycrosley/isort"
           })
diff --git a/src/beautifiers/yapf.coffee b/src/beautifiers/yapf.coffee
index 5ba490c..3ac7092 100644
--- a/src/beautifiers/yapf.coffee
+++ b/src/beautifiers/yapf.coffee
@@ -24,8 +24,12 @@ module.exports = class Yapf extends Beautifier
       }, ignoreReturnCode: true)
       .then(=>
         if options.sort_imports
+          editor = atom.workspace.getActiveTextEditor()
+          filePath = editor.getPath()
+          projectPath = atom.project.relativizePath(filePath)[0]
+
           @run("isort",
-            [tempFile],
+            ["-sp", projectPath, tempFile],
             help: {
               link: "https://github.com/timothycrosley/isort"
           })