diff --git a/modules/build/src/main/scala/scala/build/Inputs.scala b/modules/build/src/main/scala/scala/build/Inputs.scala
index 62cc86bc63..5522d35921 100644
--- a/modules/build/src/main/scala/scala/build/Inputs.scala
+++ b/modules/build/src/main/scala/scala/build/Inputs.scala
@@ -128,7 +128,8 @@ final case class Inputs(
     String.format(s"%040x", calculatedSum)
   }
 
-  private def singleFilesFromDirectory(d: Inputs.Directory): Seq[Inputs.SingleFile] =
+  private def singleFilesFromDirectory(d: Inputs.Directory): Seq[Inputs.SingleFile] = {
+    import Ordering.Implicits.seqOrdering
     os.walk.stream(d.path, skip = _.last.startsWith("."))
       .filter(os.isFile(_))
       .collect {
@@ -140,6 +141,8 @@ final case class Inputs(
           Inputs.Script(d.path, p.subRelativeTo(d.path))
       }
       .toVector
+      .sortBy(_.subPath.segments)
+  }
 }
 
 object Inputs {
@@ -175,8 +178,10 @@ object Inputs {
       ScopePath(Left(source), subPath)
   }
 
-  sealed trait SingleFile   extends OnDisk with SingleElement
-  sealed trait SourceFile   extends SingleFile
+  sealed trait SingleFile extends OnDisk with SingleElement
+  sealed trait SourceFile extends SingleFile {
+    def subPath: os.SubPath
+  }
   sealed trait Compiled     extends Element
   sealed trait AnyScalaFile extends Compiled
 
diff --git a/modules/build/src/main/scala/scala/build/Project.scala b/modules/build/src/main/scala/scala/build/Project.scala
index 5917100ba2..162213d55f 100644
--- a/modules/build/src/main/scala/scala/build/Project.scala
+++ b/modules/build/src/main/scala/scala/build/Project.scala
@@ -5,6 +5,8 @@ import _root_.coursier.{Dependency => CsDependency, core => csCore, util => csUt
 import com.github.plokhotnyuk.jsoniter_scala.core.{writeToArray => writeAsJsonToArray}
 import coursier.core.Classifier
 
+import java.io.ByteArrayOutputStream
+import java.nio.charset.StandardCharsets
 import java.nio.file.Path
 import java.util.Arrays
 
@@ -68,17 +70,46 @@ final case class Project(
   def bloopFile: BloopConfig.File =
     BloopConfig.File(BloopConfig.File.LatestVersion, bloopProject)
 
+  private def maybeUpdateInputs(logger: Logger): Boolean = {
+    val dest = directory / ".bloop" / s"$projectName.inputs.txt"
+    val onDiskOpt =
+      if (os.exists(dest)) Some(os.read.bytes(dest))
+      else None
+    val newContent = {
+      val linesIt =
+        if (sources.forall(_.startsWith(workspace)))
+          sources.iterator.map(_.relativeTo(workspace).toString)
+        else
+          sources.iterator.map(_.toString)
+      val it = linesIt.map(_ + System.lineSeparator()).map(_.getBytes(StandardCharsets.UTF_8))
+      val b  = new ByteArrayOutputStream
+      for (elem <- it)
+        b.write(elem)
+      b.toByteArray()
+    }
+    val doWrite = onDiskOpt.forall(onDisk => !Arrays.equals(onDisk, newContent))
+    if (doWrite) {
+      logger.debug(s"Writing source file list in $dest")
+      os.write.over(dest, newContent, createFolders = true)
+    }
+    else
+      logger.debug(s"Source file list in $dest doesn't need updating")
+    doWrite
+  }
+
   def writeBloopFile(strictCheck: Boolean, logger: Logger): Boolean = {
     lazy val bloopFileContent =
       writeAsJsonToArray(bloopFile)(BloopCodecs.codecFile)
     val dest = directory / ".bloop" / s"$projectName.json"
-    val doWrite = !os.isFile(dest) || {
-      strictCheck && {
-        logger.debug(s"Checking Bloop project in $dest")
-        val currentContent = os.read.bytes(dest)
-        !Arrays.equals(currentContent, bloopFileContent)
-      }
-    }
+    val doWrite =
+      if (strictCheck)
+        !os.isFile(dest) || {
+          logger.debug(s"Checking Bloop project in $dest")
+          val currentContent = os.read.bytes(dest)
+          !Arrays.equals(currentContent, bloopFileContent)
+        }
+      else
+        maybeUpdateInputs(logger) || !os.isFile(dest)
     if (doWrite) {
       logger.debug(s"Writing bloop project in $dest")
       os.write.over(dest, bloopFileContent, createFolders = true)
diff --git a/project/settings.sc b/project/settings.sc
index 152602d7f4..5b418114e1 100644
--- a/project/settings.sc
+++ b/project/settings.sc
@@ -783,7 +783,8 @@ trait ScalaCliCompile extends ScalaModule {
                   asOpt("--jar", compileClasspath().map(_.path)),
                   asOpt("-O", scalacPluginClasspath().map(p => s"-Xplugin:${p.path}")),
                   Seq("--jvm", "zulu:17"),
-                  "--strict-bloop-json-check=false", // don't check Bloop JSON files at each run
+                  // re-enable this when switching to Scala CLI > 0.1.2
+                  // "--strict-bloop-json-check=false", // don't check Bloop JSON files at each run
                   workspace,
                   sourceFiles
                 )