diff --git a/metals/src/main/scala/scala/meta/internal/builds/BuildTools.scala b/metals/src/main/scala/scala/meta/internal/builds/BuildTools.scala
index 620d0b53173..5f2196281f5 100644
--- a/metals/src/main/scala/scala/meta/internal/builds/BuildTools.scala
+++ b/metals/src/main/scala/scala/meta/internal/builds/BuildTools.scala
@@ -121,21 +121,40 @@ final class BuildTools(
   )
   def isBazel: Boolean = bazelProject.isDefined
 
+  private def customProjectRoot =
+    userConfig().customProjectRoot
+      .map(_.trim() match {
+        case "." => workspace
+        case relativePath => workspace.resolve(relativePath)
+      })
+      .filter { projectRoot =>
+        val exists = projectRoot.exists
+        if (!exists) {
+          scribe.error(s"custom project root $projectRoot does not exist")
+        }
+        exists
+      }
+
   private def searchForBuildTool(
       isProjectRoot: AbsolutePath => Boolean
-  ): Option[AbsolutePath] =
-    if (isProjectRoot(workspace)) Some(workspace)
-    else
-      workspace.toNIO
-        .toFile()
-        .listFiles()
-        .collectFirst {
-          case file
-              if file.isDirectory &&
-                !file.getName.startsWith(".") &&
-                isProjectRoot(AbsolutePath(file.toPath())) =>
-            AbsolutePath(file.toPath())
-        }
+  ): Option[AbsolutePath] = {
+    customProjectRoot match {
+      case Some(projectRoot) => Some(projectRoot).filter(isProjectRoot)
+      case None =>
+        if (isProjectRoot(workspace)) Some(workspace)
+        else
+          workspace.toNIO
+            .toFile()
+            .listFiles()
+            .collectFirst {
+              case file
+                  if file.isDirectory &&
+                    !file.getName.startsWith(".") &&
+                    isProjectRoot(AbsolutePath(file.toPath())) =>
+                AbsolutePath(file.toPath())
+            }
+    }
+  }
 
   def allAvailable: List[BuildTool] = {
     List(
diff --git a/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala b/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala
index 8ba4ebc850d..4c87355b9b2 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/MetalsLspService.scala
@@ -957,6 +957,13 @@ class MetalsLspService(
       compilers.restartAll()
     }
 
+    val slowConnect =
+      if (userConfig.customProjectRoot != old.customProjectRoot) {
+        tables.buildTool.reset()
+        tables.buildServers.reset()
+        slowConnectToBuildServer(false).ignoreValue
+      } else Future.successful(())
+
     val resetDecorations =
       if (
         userConfig.showImplicitArguments != old.showImplicitArguments ||
@@ -1008,11 +1015,10 @@ class MetalsLspService(
       }
       .getOrElse(Future.successful(()))
 
-    Future
-      .sequence(
-        List(restartBuildServer, resetDecorations)
-      )
-      .map(_ => ())
+    for {
+      _ <- slowConnect
+      _ <- Future.sequence(List(restartBuildServer, resetDecorations))
+    } yield ()
   }
 
   override def didOpen(
diff --git a/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala b/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala
index e9707c42b89..e22ed45bced 100644
--- a/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala
+++ b/metals/src/main/scala/scala/meta/internal/metals/UserConfiguration.scala
@@ -53,6 +53,7 @@ case class UserConfiguration(
     testUserInterface: TestUserInterfaceKind = TestUserInterfaceKind.CodeLenses,
     javaFormatConfig: Option[JavaFormatConfig] = None,
     scalafixRulesDependencies: List[String] = Nil,
+    customProjectRoot: Option[String] = None,
     scalaCliLauncher: Option[String] = None,
 ) {
 
@@ -313,6 +314,14 @@ object UserConfiguration {
           |launcher, not available in PATH.
           |""".stripMargin,
       ),
+      UserConfigurationOption(
+        "custom-project-root",
+        """empty string `""`.""",
+        """"backend/scalaProject/"""",
+        "Scala CLI launcher",
+        """Optional relative path to your project's root.
+          |If you want your project root to be the workspace/workspace root set it to "." .""".stripMargin,
+      ),
     )
 
   def fromJson(
@@ -525,6 +534,8 @@ object UserConfiguration {
     val scalafixRulesDependencies =
       getStringListKey("scalafix-rules-dependencies").getOrElse(Nil)
 
+    val customProjectRoot = getStringKey("custom-project-root")
+
     if (errors.isEmpty) {
       Right(
         UserConfiguration(
@@ -555,6 +566,7 @@ object UserConfiguration {
           disableTestCodeLenses,
           javaFormatConfig,
           scalafixRulesDependencies,
+          customProjectRoot,
         )
       )
     } else {
diff --git a/tests/slow/src/test/scala/tests/CustomProjectRootLspSuite.scala b/tests/slow/src/test/scala/tests/CustomProjectRootLspSuite.scala
new file mode 100644
index 00000000000..7bffad312c1
--- /dev/null
+++ b/tests/slow/src/test/scala/tests/CustomProjectRootLspSuite.scala
@@ -0,0 +1,37 @@
+package tests
+import scala.meta.internal.metals.UserConfiguration
+import scala.meta.internal.metals.{BuildInfo => V}
+
+class CustomProjectRootLspSuite
+    extends BaseLspSuite("custom-project-root", BloopImportInitializer) {
+  override def userConfig: UserConfiguration =
+    UserConfiguration().copy(customProjectRoot = Some("inner/inner/"))
+
+  test("basic") {
+    cleanWorkspace()
+    for {
+      _ <- initialize(
+        s"""|/build.sbt
+            |scalaVersion := "${V.scala213}"
+            |/inner/inner/project.scala
+            |//> using scala ${V.scala3}
+            |/inner/inner/Main.scala
+            |package a
+            |
+            |val k = 1
+            |val m: Int = "aaa"
+            |""".stripMargin
+      )
+      _ <- server.didOpen("inner/inner/Main.scala")
+      _ = assert(server.server.bspSession.exists(_.main.isScalaCLI))
+      _ = assertEquals(
+        client.workspaceDiagnostics,
+        """|inner/inner/Main.scala:4:14: error: Found:    ("aaa" : String)
+           |Required: Int
+           |val m: Int = "aaa"
+           |             ^^^^^
+           |""".stripMargin,
+      )
+    } yield ()
+  }
+}