diff --git a/programs/server/Server.cpp b/programs/server/Server.cpp
index 188dd2c019d..bb23e10770e 100644
--- a/programs/server/Server.cpp
+++ b/programs/server/Server.cpp
@@ -628,7 +628,8 @@ void loadStartupScripts(const Poco::Util::AbstractConfiguration & config, Contex
                 auto condition_write_buffer = WriteBufferFromOwnString();
 
                 LOG_DEBUG(log, "Checking startup query condition `{}`", condition);
-                executeQuery(condition_read_buffer, condition_write_buffer, true, context, callback, QueryFlags{ .internal = true }, std::nullopt, {});
+                auto startup_context = Context::createCopy(context);
+                executeQuery(condition_read_buffer, condition_write_buffer, true, startup_context, callback, QueryFlags{ .internal = true }, std::nullopt, {});
 
                 auto result = condition_write_buffer.str();
 
@@ -648,7 +649,8 @@ void loadStartupScripts(const Poco::Util::AbstractConfiguration & config, Contex
             auto write_buffer = WriteBufferFromOwnString();
 
             LOG_DEBUG(log, "Executing query `{}`", query);
-            executeQuery(read_buffer, write_buffer, true, context, callback, QueryFlags{ .internal = true }, std::nullopt, {});
+            auto startup_context = Context::createCopy(context);
+            executeQuery(read_buffer, write_buffer, true, startup_context, callback, QueryFlags{ .internal = true }, std::nullopt, {});
         }
     }
     catch (...)
diff --git a/tests/integration/test_startup_scripts/configs/config.d/startup_scripts.xml b/tests/integration/test_startup_scripts/configs/config.d/startup_scripts.xml
index e8a711a926a..21d2865efe8 100644
--- a/tests/integration/test_startup_scripts/configs/config.d/startup_scripts.xml
+++ b/tests/integration/test_startup_scripts/configs/config.d/startup_scripts.xml
@@ -13,5 +13,13 @@
         <scripts>
             <query>SELECT * FROM system.query_log LIMIT 1</query>
         </scripts>
+        <scripts>
+            <query>SELECT 1 SETTINGS skip_unavailable_shards = 1</query>
+            <condition>SELECT 1;</condition>
+        </scripts>
+        <scripts>
+            <query>SELECT 1 SETTINGS skip_unavailable_shards = 1</query>
+            <condition>SELECT 1;</condition>
+        </scripts>
     </startup_scripts>
 </clickhouse>
diff --git a/tests/integration/test_startup_scripts/test.py b/tests/integration/test_startup_scripts/test.py
index 43a871a6fc5..ee1b34bcf24 100644
--- a/tests/integration/test_startup_scripts/test.py
+++ b/tests/integration/test_startup_scripts/test.py
@@ -16,6 +16,7 @@ def test_startup_scripts():
     try:
         cluster.start()
         assert node.query("SHOW TABLES") == "TestTable\n"
+        assert node.query("SELECT value, changed FROM system.settings WHERE name = 'skip_unavailable_shards'") == "0\t0\n"
 
     finally:
         cluster.shutdown()