diff --git a/plugin/src/main/scala/org/scalafmt/sbt/ScalafmtPlugin.scala b/plugin/src/main/scala/org/scalafmt/sbt/ScalafmtPlugin.scala
index 411bc12..5bf4176 100644
--- a/plugin/src/main/scala/org/scalafmt/sbt/ScalafmtPlugin.scala
+++ b/plugin/src/main/scala/org/scalafmt/sbt/ScalafmtPlugin.scala
@@ -176,15 +176,19 @@ object ScalafmtPlugin extends AutoPlugin {
     @inline private def asRelative(file: File): File =
       file.relativeTo(baseDir).getOrElse(file)
 
-    private def filterFiles(sources: Seq[File]): Seq[File] = {
-      val filter = getFileFilter()
-      sources.distinct.filter { file =>
-        val path = file.toPath.toAbsolutePath
-        scalafmtSession.matchesProjectFilters(path) && filter(path)
+    private def filterFiles(sources: Seq[File], dirs: Seq[File]): Seq[File] = {
+      val filter = getFileFilter(dirs)
+      sources.distinct.flatMap { file =>
+        val canonFile = file.getCanonicalFile
+        val path = canonFile.toPath.toAbsolutePath
+        val ok = scalafmtSession.matchesProjectFilters(path) && filter(path)
+        if (ok) Some(canonFile) else None
       }
     }
 
-    private def getFileFilter(): Path => Boolean = {
+    private def getFileFilter(dirs: Seq[File]): Path => Boolean = {
+      // dirs don't have to be within baseDir but within the same git tree
+      def absDirs = dirs.map(x => AbsoluteFile(x.toPath))
       def gitOps = GitOps.FactoryImpl(AbsoluteFile(baseDir.toPath))
       def getFromFiles(getFiles: => Seq[AbsoluteFile], gitCmd: => String) = {
         def gitMessage = s"[git $gitCmd] ($baseDir)"
@@ -199,12 +203,12 @@ object ScalafmtPlugin extends AutoPlugin {
       }
 
       if (filterMode == FilterMode.diffDirty)
-        getFromFiles(gitOps.status(), "status")
+        getFromFiles(gitOps.status(absDirs: _*), "status")
       else if (filterMode.startsWith(FilterMode.diffRefPrefix)) {
         val branch = filterMode.substring(FilterMode.diffRefPrefix.length)
-        getFromFiles(gitOps.diff(branch), s"diff $branch")
+        getFromFiles(gitOps.diff(branch, absDirs: _*), s"diff $branch")
       } else if (filterMode != FilterMode.none && scalafmtSession.isGitOnly)
-        getFromFiles(gitOps.lsTree(), "ls-files")
+        getFromFiles(gitOps.lsTree(absDirs: _*), "ls-files")
       else {
         log.debug("considering all files (no git)")
         _ => true
@@ -244,8 +248,8 @@ object ScalafmtPlugin extends AutoPlugin {
       res
     }
 
-    def formatTrackedSources(sources: Seq[File]): Unit = {
-      val filteredSources = filterFiles(sources)
+    def formatTrackedSources(sources: Seq[File], dirs: Seq[File]): Unit = {
+      val filteredSources = filterFiles(sources, dirs)
       trackSourcesAndConfig(cacheStoreFactory, filteredSources) {
         (outDiff, configChanged, prev) =>
           val filesToFormat: Seq[File] =
@@ -261,8 +265,8 @@ object ScalafmtPlugin extends AutoPlugin {
       }
     }
 
-    def formatSources(sources: Seq[File]): Unit =
-      formatFilteredSources(filterFiles(sources))
+    def formatSources(sources: Seq[File], dirs: Seq[File]): Unit =
+      formatFilteredSources(filterFiles(sources, dirs))
 
     private def formatFilteredSources(sources: Seq[File]): Unit = {
       if (sources.nonEmpty)
@@ -274,8 +278,8 @@ object ScalafmtPlugin extends AutoPlugin {
       if (cnt > 0) log.info(s"Reformatted $cnt Scala sources")
     }
 
-    def checkTrackedSources(sources: Seq[File]): Unit = {
-      val filteredSources = filterFiles(sources)
+    def checkTrackedSources(sources: Seq[File], dirs: Seq[File]): Unit = {
+      val filteredSources = filterFiles(sources, dirs)
       val result = trackSourcesAndConfig(cacheStoreFactory, filteredSources) {
         (outDiff, configChanged, prev) =>
           val filesToCheck: Seq[File] =
@@ -300,8 +304,8 @@ object ScalafmtPlugin extends AutoPlugin {
       throwOnFailure(result)
     }
 
-    def checkSources(sources: Seq[File]): Unit =
-      throwOnFailure(checkFilteredSources(filterFiles(sources)))
+    def checkSources(sources: Seq[File], dirs: Seq[File]): Unit =
+      throwOnFailure(checkFilteredSources(filterFiles(sources, dirs)))
 
     private def checkFilteredSources(sources: Seq[File]): ScalafmtAnalysis = {
       if (sources.nonEmpty) {
@@ -393,57 +397,69 @@ object ScalafmtPlugin extends AutoPlugin {
     }
   }
 
-  private def scalafmtTask(sources: Seq[File], session: FormatSession) =
+  private def scalafmtTask(
+      sources: Seq[File],
+      dirs: Seq[File],
+      session: FormatSession
+  ) =
     Def.task {
-      session.formatTrackedSources(sources)
+      session.formatTrackedSources(sources, dirs)
     } tag (ScalafmtTagPack: _*)
 
-  private def scalafmtCheckTask(sources: Seq[File], session: FormatSession) =
+  private def scalafmtCheckTask(
+      sources: Seq[File],
+      dirs: Seq[File],
+      session: FormatSession
+  ) =
     Def.task {
-      session.checkTrackedSources(sources)
+      session.checkTrackedSources(sources, dirs)
     } tag (ScalafmtTagPack: _*)
 
   private def getScalafmtSourcesTask(
-      f: (Seq[File], FormatSession) => InitTask
+      f: (Seq[File], Seq[File], FormatSession) => InitTask
   ) = Def.taskDyn[Unit] {
     val sources = (unmanagedSources in scalafmt).?.value.getOrElse(Seq.empty)
-    getScalafmtTask(f)(sources, scalaConfig.value)
+    val dirs = (unmanagedSourceDirectories in scalafmt).?.value.getOrElse(Nil)
+    getScalafmtTask(f)(sources, dirs, scalaConfig.value)
   }
 
   private def scalafmtSbtTask(
       sources: Seq[File],
+      dirs: Seq[File],
       session: FormatSession
   ) = Def.task {
-    session.formatSources(sources)
+    session.formatSources(sources, dirs)
   } tag (ScalafmtTagPack: _*)
 
   private def scalafmtSbtCheckTask(
       sources: Seq[File],
+      dirs: Seq[File],
       session: FormatSession
   ) = Def.task {
-    session.checkSources(sources)
+    session.checkSources(sources, dirs)
   } tag (ScalafmtTagPack: _*)
 
   private def getScalafmtSbtTasks(
-      func: (Seq[File], FormatSession) => InitTask
+      func: (Seq[File], Seq[File], FormatSession) => InitTask
   ) = Def.taskDyn {
     joinScalafmtTasks(func)(
-      (sbtSources.value, sbtConfig.value),
-      (metabuildSources.value, scalaConfig.value)
+      (sbtSources.value, Nil, sbtConfig.value),
+      (metabuildSources.value, Nil, scalaConfig.value)
     )
   }
 
   private def joinScalafmtTasks(
-      func: (Seq[File], FormatSession) => InitTask
-  )(tuples: (Seq[File], Path)*) = {
-    val tasks = tuples
-      .map { case (files, config) => getScalafmtTask(func)(files, config) }
+      func: (Seq[File], Seq[File], FormatSession) => InitTask
+  )(tuples: (Seq[File], Seq[File], Path)*) = {
+    val tasks = tuples.map { case (files, dirs, config) =>
+      getScalafmtTask(func)(files, dirs, config)
+    }
     Def.sequential(tasks.tail.toList, tasks.head)
   }
 
   private def getScalafmtTask(
-      func: (Seq[File], FormatSession) => InitTask
-  )(files: Seq[File], config: Path) = Def.taskDyn[Unit] {
+      func: (Seq[File], Seq[File], FormatSession) => InitTask
+  )(files: Seq[File], dirs: Seq[File], config: Path) = Def.taskDyn[Unit] {
     if (files.isEmpty) Def.task(Unit)
     else {
       val session = new FormatSession(
@@ -460,7 +476,7 @@ object ScalafmtPlugin extends AutoPlugin {
           scalafmtDetailedError.value
         )
       )
-      func(files, session)
+      func(files, dirs, session)
     }
   }
 
@@ -505,7 +521,7 @@ object ScalafmtPlugin extends AutoPlugin {
           scalafmtFailOnErrors.value,
           scalafmtDetailedError.value
         )
-      ).formatSources(absFiles)
+      ).formatSources(absFiles, Nil)
     }
   )
 
diff --git a/plugin/src/sbt-test/scalafmt-sbt/sbt/test b/plugin/src/sbt-test/scalafmt-sbt/sbt/test
index 3e73192..a305e2f 100644
--- a/plugin/src/sbt-test/scalafmt-sbt/sbt/test
+++ b/plugin/src/sbt-test/scalafmt-sbt/sbt/test
@@ -202,7 +202,7 @@ $ exec git -C p19 add "jvm/src/main/scala/TestGood.scala"
 > p19/scalafmtCheck
 $ copy-file changes/invalid.scala p19/shared/src/main/scala/TestInvalid1.scala
 $ exec git -C p19 add "shared/src/main/scala/TestInvalid1.scala"
-> p19/scalafmtCheck
+-> p19/scalafmtCheck
 
 $ copy-file changes/target/managed.scala project/target/managed.scala
 $ copy-file changes/x/Something.scala project/x/Something.scala