diff --git a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
index 39d3c2e173..fd5a4969b0 100644
--- a/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
+++ b/plugins/nf-tower/src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy
@@ -74,14 +74,13 @@ class LogsCheckpoint implements TraceObserverV2 {
         log.debug "Starting logs checkpoint thread - interval: ${interval}"
         try {
             while( true ) {
-                await(interval)
-                if( Thread.currentThread().isInterrupted() )
-                    break
+                final interrupted = await(interval)
+                Thread.interrupted()  // clear flag so NIO writes in saveFiles() succeed
                 synchronized(lock) {
-                    if( Thread.currentThread().isInterrupted() )
-                        break
                     handler.saveFiles()
                 }
+                if( interrupted )
+                    break
             }
         }
         finally {
@@ -89,13 +88,14 @@ class LogsCheckpoint implements TraceObserverV2 {
         }
     }
 
-    protected void await(Duration interval) {
+    protected boolean await(Duration interval) {
         try {
             Thread.sleep(interval.toMillis())
+            return Thread.currentThread().isInterrupted()
         }
         catch (InterruptedException e) {
             log.debug "Interrupted logs checkpoint thread"
-            Thread.currentThread().interrupt()
+            return true
         }
     }
 }
diff --git a/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy
index 4115a32637..ff37c36483 100644
--- a/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy
+++ b/plugins/nf-tower/src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy
@@ -80,4 +80,26 @@ class LogsCheckpointTest extends Specification {
         cleanup:
         SysEnv.pop()
     }
+
+    def 'should perform final saveFiles when interrupted mid-sleep' () {
+        given:
+        SysEnv.push(TOWER_LOGS_CHECKPOINT_INTERVAL: '60s')
+        def session = Mock(Session) {
+            getWorkDir() >> TestHelper.createInMemTempDir()
+            getConfig() >> [:]
+        }
+        def handler = Mock(LogsHandler)
+        def checkpoint = new LogsCheckpoint()
+
+        when:
+        checkpoint.onFlowCreate(session)
+        checkpoint.@handler = handler   // inject mock before thread wakes up
+        checkpoint.onFlowComplete()
+
+        then:
+        1 * handler.saveFiles() >> { assert !Thread.currentThread().isInterrupted() }
+
+        cleanup:
+        SysEnv.pop()
+    }
 }