diff --git a/main/src/main/scala/sbt/internal/server/BuildServerProtocol.scala b/main/src/main/scala/sbt/internal/server/BuildServerProtocol.scala
index 0853d83c5..401bf6d31 100644
--- a/main/src/main/scala/sbt/internal/server/BuildServerProtocol.scala
+++ b/main/src/main/scala/sbt/internal/server/BuildServerProtocol.scala
@@ -194,7 +194,13 @@ object BuildServerProtocol {
       val filter = ScopeFilter.in(workspace.scopes.values.toList)
       Def.task {
         val results = Keys.clean.result.all(filter).value
-        val cleaned = anyOrThrow(results).size == targets.size
+        val successes = anyOrThrow(results).size
+
+        // When asking to Rebuild Project, IntelliJ sends the root build as an additional target, however it is
+        // not returned as part of the results. In this case, there's 1 build entry in the workspace, and we're
+        // checking that the executed results plus this entry is equal to the total number of targets.
+        // When rebuilding a single module, the root build isn't sent, just the requested targets.
+        val cleaned = successes + workspace.builds.size == targets.size
         s.respondEvent(CleanCacheResult(None, cleaned))
       }
     }.evaluated,
diff --git a/server-test/src/test/scala/testpkg/BuildServerTest.scala b/server-test/src/test/scala/testpkg/BuildServerTest.scala
index d29a8c880..d54659038 100644
--- a/server-test/src/test/scala/testpkg/BuildServerTest.scala
+++ b/server-test/src/test/scala/testpkg/BuildServerTest.scala
@@ -138,6 +138,26 @@ object BuildServerTest extends AbstractServerTest {
     assert(targetDir.list().isEmpty)
   }
 
+  test("buildTarget/cleanCache: rebuild project") { _ =>
+    svr.sendJsonRpc(
+      """{ "jsonrpc": "2.0", "id": "45", "method": "workspace/buildTargets", "params": {} }"""
+    )
+    assert(processing("workspace/buildTargets"))
+    val result = svr.waitFor[WorkspaceBuildTargetsResult](10.seconds)
+    val allTargets = result.targets.map(_.id.uri)
+
+    svr.sendJsonRpc(
+      s"""{ "jsonrpc": "2.0", "id": "46", "method": "buildTarget/cleanCache", "params": {
+         |  "targets": [
+         |    ${allTargets.map(uri => s"""{ "uri": "$uri" }""").mkString(",\n")}
+         |  ]
+         |} }""".stripMargin
+    )
+    assert(processing("buildTarget/cleanCache"))
+    val res = svr.waitFor[CleanCacheResult](10.seconds)
+    assert(res.cleaned)
+  }
+
   test("workspace/reload") { _ =>
     svr.sendJsonRpc(
       """{ "jsonrpc": "2.0", "id": "48", "method": "workspace/reload"}"""