diff --git a/tests/integration/test_jbod_balancer/test.py b/tests/integration/test_jbod_balancer/test.py
index 28eee63a088b..8c2966ff0564 100644
--- a/tests/integration/test_jbod_balancer/test.py
+++ b/tests/integration/test_jbod_balancer/test.py
@@ -9,6 +9,7 @@
 import pytest
 from helpers.client import QueryRuntimeException
 from helpers.cluster import ClickHouseCluster
+from helpers.wait_for_helpers import wait_for_merges
 
 cluster = ClickHouseCluster(__file__)
 
@@ -67,7 +68,7 @@ def check_balance(node, table):
                 partition, disk_name
         )
         GROUP BY partition
-        HAVING gini < 0.2
+        HAVING gini < 0.1
         """.format(
             table
         )
@@ -76,6 +77,20 @@ def check_balance(node, table):
     assert set(partitions) == set(["0", "1"])
 
 
+def wait_until_fully_merged(node, table, retry=20):
+    for i in range(retry):
+        # Wait in-flight merges
+        wait_for_merges(node, table)
+
+        # Check if we can assign new merges
+        try:
+            node.query(f"optimize table {table} settings optimize_throw_if_noop = 1")
+        except e:
+            return
+
+    raise Exception(f"There are still merges on-going after {retry} assignments")
+
+
 def test_jbod_balanced_merge(start_cluster):
     try:
         node1.query(
@@ -110,7 +125,7 @@ def task(i):
 
         p.map(task, range(200))
 
-        time.sleep(1)
+        wait_until_fully_merged(node1, "tbl")
 
         check_balance(node1, "tbl")
 
@@ -183,6 +198,8 @@ def task(i):
 
         p.map(task, range(200))
 
+        wait_until_fully_merged(node1, "tbl")
+
         node2.query("SYSTEM SYNC REPLICA tbl", timeout=10)
 
         check_balance(node1, "tbl")