diff --git a/main/src/main/scala/sbt/Main.scala b/main/src/main/scala/sbt/Main.scala
index 4db35148f..8f3ee4584 100644
--- a/main/src/main/scala/sbt/Main.scala
+++ b/main/src/main/scala/sbt/Main.scala
@@ -61,6 +61,7 @@ private[sbt] object xMain:
 
   private[sbt] def run(configuration: xsbti.AppConfiguration): xsbti.MainResult = boundary {
     try {
+      if (!sys.props.contains("jna.nosys")) sys.props.put("jna.nosys", "true")
       import BasicCommandStrings.{ JavaClient, DashDashClient, DashDashServer, runEarly }
       import BasicCommands.early
       import BuiltinCommands.defaults
@@ -265,7 +266,7 @@ object StandardMain {
       preCommands: Seq[String]
   ): State = {
     // This is to workaround https://github.com/sbt/io/issues/110
-    sys.props.put("jna.nosys", "true")
+    if (!sys.props.contains("jna.nosys")) sys.props.put("jna.nosys", "true")
 
     import BasicCommandStrings.{ DashDashDetachStdio, DashDashServer, isEarlyCommand }
     val userCommands =
diff --git a/project/Scripted.scala b/project/Scripted.scala
index de692d210..9bd2f3649 100644
--- a/project/Scripted.scala
+++ b/project/Scripted.scala
@@ -25,7 +25,7 @@ trait ScriptedKeys {
 
 object Scripted {
   // This is to workaround https://github.com/sbt/io/issues/110
-  sys.props.put("jna.nosys", "true")
+  if (!sys.props.contains("jna.nosys")) sys.props.put("jna.nosys", "true")
 
   val RepoOverrideTest = config("repoOverrideTest") extend Compile
 
diff --git a/sbt-app/src/test/scala/sbt/RunFromSourceMain.scala b/sbt-app/src/test/scala/sbt/RunFromSourceMain.scala
index 8919cee30..d0f8e7ca9 100644
--- a/sbt-app/src/test/scala/sbt/RunFromSourceMain.scala
+++ b/sbt-app/src/test/scala/sbt/RunFromSourceMain.scala
@@ -56,7 +56,7 @@ object RunFromSourceMain {
         s"Must specify working directory, scala version and sbt version and classpath as the first three arguments"
       )
     case Array(wd, scalaVersion, sbtVersion, classpath, args*) =>
-      System.setProperty("jna.nosys", "true")
+      if (System.getProperty("jna.nosys") == null) System.setProperty("jna.nosys", "true")
       if (args.exists(_.startsWith("<"))) System.setProperty("sbt.io.virtual", "false")
       val context = LoggerContext()
       try run(file(wd), scalaVersion, sbtVersion, classpath, args, context)