diff --git a/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/bep/BepServer.kt b/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/bep/BepServer.kt
index b62e1298d..e73674ced 100644
--- a/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/bep/BepServer.kt
+++ b/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/bep/BepServer.kt
@@ -100,6 +100,9 @@ class BepServer(
 
   private fun processProgressEvent(event: BuildEventStreamProtos.BuildEvent) {
     if (event.hasProgress()) {
+      if (target != null) {
+        processDiagnosticText(event.progress.stderr, target.uri, true)
+      }
       // TODO https://youtrack.jetbrains.com/issue/BAZEL-622
       // bepLogger.onProgress(event.getProgress());
     }
@@ -185,7 +188,7 @@ class BepServer(
         try {
           val path = Paths.get(URI.create(actionEvent.stderr.uri))
           val stdErrText = Files.readString(path)
-          processDiagnosticText(stdErrText, label)
+          processDiagnosticText(stdErrText, label, false)
         } catch (e: FileSystemNotFoundException) {
           LOGGER.warn(e)
         } catch (e: IOException) {
@@ -193,24 +196,26 @@ class BepServer(
         }
       }
       BuildEventStreamProtos.File.FileCase.CONTENTS -> {
-        processDiagnosticText(actionEvent.stderr.contents.toStringUtf8(), label)
+        processDiagnosticText(actionEvent.stderr.contents.toStringUtf8(), label, false)
       }
       else -> {
-        processDiagnosticText("", label)
+        processDiagnosticText("", label, false)
       }
     }
   }
 
-  private fun processDiagnosticText(stdErrText: String, targetLabel: String) {
-    val events =
-      diagnosticsService.extractDiagnostics(
-        stdErrText, targetLabel, startedEvents.first.value
-      )
-    events.forEach(Consumer { publishDiagnosticsParams: PublishDiagnosticsParams? ->
-      bspClient.onBuildPublishDiagnostics(
-        publishDiagnosticsParams
-      )
-    })
+  private fun processDiagnosticText(stdErrText: String, targetLabel: String, diagnosticsFromProgress: Boolean) {
+    if (startedEvents.isNotEmpty() && stdErrText.isNotEmpty()) {
+      val events =
+        diagnosticsService.extractDiagnostics(
+          stdErrText, targetLabel, startedEvents.first.value, diagnosticsFromProgress
+        )
+      events.forEach(Consumer { publishDiagnosticsParams: PublishDiagnosticsParams? ->
+        bspClient.onBuildPublishDiagnostics(
+            publishDiagnosticsParams
+        )
+      })
+    }
   }
 
   private fun consumeCompletedEvent(event: BuildEventStreamProtos.BuildEvent) {
diff --git a/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsParser.kt b/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsParser.kt
index 4ffec6f07..bee8cafdf 100644
--- a/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsParser.kt
+++ b/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsParser.kt
@@ -2,9 +2,9 @@ package org.jetbrains.bsp.bazel.server.diagnostics
 
 class DiagnosticsParser {
 
-  fun parse(bazelOutput: String, target: String): List<Diagnostic> {
+  fun parse(bazelOutput: String, target: String, onlyKnownFiles: Boolean): List<Diagnostic> {
     val output = prepareOutput(bazelOutput, target)
-    val diagnostics = collectDiagnostics(output)
+    val diagnostics = collectDiagnostics(output, onlyKnownFiles)
     return deduplicate(diagnostics)
   }
 
@@ -14,7 +14,7 @@ class DiagnosticsParser {
     return Output(relevantLines, target)
   }
 
-  private fun collectDiagnostics(output: Output): List<Diagnostic> {
+  private fun collectDiagnostics(output: Output, onlyKnownFiles: Boolean): List<Diagnostic> {
     val diagnostics = mutableListOf<Diagnostic>()
     while (output.nonEmpty()) {
       for (parser in Parsers) {
@@ -26,7 +26,7 @@ class DiagnosticsParser {
       }
     }
 
-    if (diagnostics.isEmpty()) {
+    if (diagnostics.isEmpty() && !onlyKnownFiles) {
       diagnostics.add(
         Diagnostic(
           position = Position(0, 0),
diff --git a/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsService.kt b/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsService.kt
index 0bb999263..6e22186d4 100644
--- a/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsService.kt
+++ b/server/src/main/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsService.kt
@@ -1,11 +1,9 @@
 package org.jetbrains.bsp.bazel.server.diagnostics
 
 import ch.epfl.scala.bsp4j.BuildTargetIdentifier
-import ch.epfl.scala.bsp4j.Diagnostic
 import ch.epfl.scala.bsp4j.PublishDiagnosticsParams
 import ch.epfl.scala.bsp4j.TextDocumentIdentifier
 import java.nio.file.Path
-import java.util.concurrent.ConcurrentHashMap
 import java.util.Collections
 
 /**
@@ -17,16 +15,20 @@ class DiagnosticsService(workspaceRoot: Path, private val hasAnyProblems: Mutabl
 
     private val parser = DiagnosticsParser()
     private val mapper = DiagnosticBspMapper(workspaceRoot)
+    /* Warnings are reported before the target completed event, when everything is cleared. so we want to avoid removing them */
+    private val updatedInThisRun = mutableSetOf<PublishDiagnosticsParams>()
 
     fun getBspState() = Collections.unmodifiableMap(hasAnyProblems)
 
     fun extractDiagnostics(
         bazelOutput: String,
         targetLabel: String,
-        originId: String?
+        originId: String?,
+        diagnosticsFromProgress: Boolean
     ): List<PublishDiagnosticsParams> {
-        val parsedDiagnostics = parser.parse(bazelOutput, targetLabel)
+        val parsedDiagnostics = parser.parse(bazelOutput, targetLabel, diagnosticsFromProgress)
         val events = mapper.createDiagnostics(parsedDiagnostics, originId)
+        if (diagnosticsFromProgress) updatedInThisRun.addAll(events)
         updateProblemState(events)
         return events
     }
@@ -34,6 +36,10 @@ class DiagnosticsService(workspaceRoot: Path, private val hasAnyProblems: Mutabl
     fun clearFormerDiagnostics(targetLabel: String): List<PublishDiagnosticsParams> {
 	    val docs = hasAnyProblems[targetLabel]
 	    hasAnyProblems.remove(targetLabel)
+        if (updatedInThisRun.isNotEmpty()) {
+            hasAnyProblems[targetLabel] = updatedInThisRun.map { it.textDocument }.toSet()
+            updatedInThisRun.clear()
+        }
 	    return docs
 	      ?.map { PublishDiagnosticsParams(it, BuildTargetIdentifier(targetLabel), emptyList(), true)}
 	      .orEmpty()
diff --git a/server/src/test/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsServiceTest.kt b/server/src/test/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsServiceTest.kt
index 9d9c2eec5..04a00a353 100644
--- a/server/src/test/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsServiceTest.kt
+++ b/server/src/test/kotlin/org/jetbrains/bsp/bazel/server/diagnostics/DiagnosticsServiceTest.kt
@@ -538,7 +538,7 @@ class DiagnosticsServiceTest {
         diagnosticsBeforeError.shouldBeEmpty()
 
         // Extract the diagnostics from BEP, there's an error in `Test.scala` of "//path/to/package:test".
-        service.extractDiagnostics(output, "//path/to/package:test", null)
+        service.extractDiagnostics(output, "//path/to/package:test", null, false)
 
         // Assert that state is updated
         service.getBspState().keys.shouldHaveSize(1)
@@ -626,8 +626,8 @@ class DiagnosticsServiceTest {
             )
         )
 
-        service.extractDiagnostics(output1, "//path/to/package:test", null)
-        service.extractDiagnostics(output2, "//path/to/package2:test", null)
+        service.extractDiagnostics(output1, "//path/to/package:test", null, false)
+        service.extractDiagnostics(output2, "//path/to/package2:test", null, false)
 
         // Assert that state is updated
         service.getBspState().keys shouldContainExactlyInAnyOrder listOf(
@@ -675,6 +675,6 @@ class DiagnosticsServiceTest {
     }
 
     private fun extractDiagnostics(output: String, buildTarget: String): List<PublishDiagnosticsParams>? {
-        return DiagnosticsService(workspacePath, ConcurrentHashMap()).extractDiagnostics(output, buildTarget, null)
+        return DiagnosticsService(workspacePath, ConcurrentHashMap()).extractDiagnostics(output, buildTarget, null, false)
     }
 }