diff --git a/test_runner/regress/test_storage_controller.py b/test_runner/regress/test_storage_controller.py
index af018f7b5d..d07fb38c5a 100644
--- a/test_runner/regress/test_storage_controller.py
+++ b/test_runner/regress/test_storage_controller.py
@@ -4158,17 +4158,12 @@ def test_storcon_create_delete_sk_down(
         env.storage_controller.stop()
         env.storage_controller.start()
 
-    config_lines = [
-        "neon.safekeeper_proto_version = 3",
-    ]
-    with env.endpoints.create("main", tenant_id=tenant_id, config_lines=config_lines) as ep:
+    with env.endpoints.create("main", tenant_id=tenant_id) as ep:
         # endpoint should start.
         ep.start(safekeeper_generation=1, safekeepers=[1, 2, 3])
         ep.safe_psql("CREATE TABLE IF NOT EXISTS t(key int, value text)")
 
-    with env.endpoints.create(
-        "child_of_main", tenant_id=tenant_id, config_lines=config_lines
-    ) as ep:
+    with env.endpoints.create("child_of_main", tenant_id=tenant_id) as ep:
         # endpoint should start.
         ep.start(safekeeper_generation=1, safekeepers=[1, 2, 3])
         ep.safe_psql("CREATE TABLE IF NOT EXISTS t(key int, value text)")
@@ -4249,17 +4244,12 @@ def test_storcon_few_sk(
 
     env.safekeepers[0].assert_log_contains(f"creating new timeline {tenant_id}/{timeline_id}")
 
-    config_lines = [
-        "neon.safekeeper_proto_version = 3",
-    ]
-    with env.endpoints.create("main", tenant_id=tenant_id, config_lines=config_lines) as ep:
+    with env.endpoints.create("main", tenant_id=tenant_id) as ep:
         # endpoint should start.
         ep.start(safekeeper_generation=1, safekeepers=safekeeper_list)
         ep.safe_psql("CREATE TABLE IF NOT EXISTS t(key int, value text)")
 
-    with env.endpoints.create(
-        "child_of_main", tenant_id=tenant_id, config_lines=config_lines
-    ) as ep:
+    with env.endpoints.create("child_of_main", tenant_id=tenant_id) as ep:
         # endpoint should start.
         ep.start(safekeeper_generation=1, safekeepers=safekeeper_list)
         ep.safe_psql("CREATE TABLE IF NOT EXISTS t(key int, value text)")
diff --git a/test_runner/regress/test_wal_acceptor.py b/test_runner/regress/test_wal_acceptor.py
index a9a6699e5c..6a7c7a8bef 100644
--- a/test_runner/regress/test_wal_acceptor.py
+++ b/test_runner/regress/test_wal_acceptor.py
@@ -2012,10 +2012,7 @@ def test_explicit_timeline_creation(neon_env_builder: NeonEnvBuilder):
     tenant_id = env.initial_tenant
     timeline_id = env.initial_timeline
 
-    config_lines = [
-        "neon.safekeeper_proto_version = 3",
-    ]
-    ep = env.endpoints.create("main", config_lines=config_lines)
+    ep = env.endpoints.create("main")
 
     # expected to fail because timeline is not created on safekeepers
     with pytest.raises(Exception, match=r".*timed out.*"):
@@ -2043,10 +2040,7 @@ def test_explicit_timeline_creation_storcon(neon_env_builder: NeonEnvBuilder):
     }
     env = neon_env_builder.init_start()
 
-    config_lines = [
-        "neon.safekeeper_proto_version = 3",
-    ]
-    ep = env.endpoints.create("main", config_lines=config_lines)
+    ep = env.endpoints.create("main")
 
     # endpoint should start.
     ep.start(safekeeper_generation=1, safekeepers=[1, 2, 3])
diff --git a/test_runner/regress/test_wal_acceptor_async.py b/test_runner/regress/test_wal_acceptor_async.py
index c5dd34f64f..4070f99568 100644
--- a/test_runner/regress/test_wal_acceptor_async.py
+++ b/test_runner/regress/test_wal_acceptor_async.py
@@ -637,10 +637,7 @@ async def quorum_sanity_single(
     # create timeline on `members_sks`
     Safekeeper.create_timeline(tenant_id, timeline_id, env.pageservers[0], mconf, members_sks)
 
-    config_lines = [
-        "neon.safekeeper_proto_version = 3",
-    ]
-    ep = env.endpoints.create(branch_name, config_lines=config_lines)
+    ep = env.endpoints.create(branch_name)
     ep.start(safekeeper_generation=1, safekeepers=compute_sks_ids)
     ep.safe_psql("create table t(key int, value text)")