diff --git a/main/src/main/scala/sbt/internal/nio/CheckBuildSources.scala b/main/src/main/scala/sbt/internal/nio/CheckBuildSources.scala
index 782975b75..a2e54fb24 100644
--- a/main/src/main/scala/sbt/internal/nio/CheckBuildSources.scala
+++ b/main/src/main/scala/sbt/internal/nio/CheckBuildSources.scala
@@ -67,14 +67,14 @@ private[sbt] object CheckBuildSources {
       @tailrec
       def projectGlobs(projectDir: File, globs: Seq[Glob]): Seq[Glob] = {
         val glob = projectDir.toGlob
-        val base = Seq(
+        val updatedGlobs = globs ++ Seq(
           glob / "*.{sbt,scala,java}",
           // We only want to recursively look in source because otherwise we have to search
           // the project target directories which is expensive.
           glob / "src" / ** / "*.{scala,java}"
         )
         val nextLevel = projectDir / "project"
-        if (nextLevel.exists) projectGlobs(nextLevel, base) else base
+        if (nextLevel.exists) projectGlobs(nextLevel, updatedGlobs) else updatedGlobs
       }
       projectGlobs(projectDir, baseDir.toGlob / "*.sbt" :: Nil)
     } else Nil
diff --git a/sbt/src/sbt-test/nio/reload/test b/sbt/src/sbt-test/nio/reload/test
index 26ef1a9ff..1d59941b2 100644
--- a/sbt/src/sbt-test/nio/reload/test
+++ b/sbt/src/sbt-test/nio/reload/test
@@ -29,3 +29,7 @@ $ copy-file changes/sub.sbt sub/build.sbt
 $ copy-file changes/ScalafmtVersion.scala project/project/ScalafmtVersion.scala
 
 > scalafmt
+
+$ delete project/plugins.sbt
+
+-> scalafmt