diff --git a/control_plane/src/local_env.rs b/control_plane/src/local_env.rs
index 47b77f0720..1b231151ce 100644
--- a/control_plane/src/local_env.rs
+++ b/control_plane/src/local_env.rs
@@ -236,7 +236,7 @@ impl Default for NeonStorageControllerConf {
             heartbeat_interval: Self::DEFAULT_HEARTBEAT_INTERVAL,
             long_reconcile_threshold: None,
             use_https_pageserver_api: false,
-            timelines_onto_safekeepers: false,
+            timelines_onto_safekeepers: true,
             use_https_safekeeper_api: false,
             use_local_compute_notifications: true,
         }
diff --git a/test_runner/fixtures/neon_fixtures.py b/test_runner/fixtures/neon_fixtures.py
index 8cf1020adb..050d61055e 100644
--- a/test_runner/fixtures/neon_fixtures.py
+++ b/test_runner/fixtures/neon_fixtures.py
@@ -489,7 +489,9 @@ class NeonEnvBuilder:
         self.config_init_force: str | None = None
         self.top_output_dir = top_output_dir
         self.control_plane_hooks_api: str | None = None
-        self.storage_controller_config: dict[Any, Any] | None = None
+        self.storage_controller_config: dict[Any, Any] | None = {
+            "timelines_onto_safekeepers": True,
+        }
 
         # Flag to enable https listener in pageserver, generate local ssl certs,
         # and force storage controller to use https for pageserver api.
@@ -4909,6 +4911,9 @@ class Safekeeper(LogUtils):
         log.info(f"finished pulling timeline from {src_ids} to {self.id}")
         return res
 
+    def safekeeper_id(self) -> SafekeeperId:
+        return SafekeeperId(self.id, "localhost", self.port.pg_tenant_only)
+
     @property
     def data_dir(self) -> Path:
         return self.env.repo_dir / "safekeepers" / f"sk{self.id}"
diff --git a/test_runner/regress/test_branching.py b/test_runner/regress/test_branching.py
index 9ce618b2ad..fa5c9aa693 100644
--- a/test_runner/regress/test_branching.py
+++ b/test_runner/regress/test_branching.py
@@ -11,6 +11,7 @@ from fixtures.common_types import Lsn, TimelineId
 from fixtures.log_helper import log
 from fixtures.pageserver.http import PageserverApiException
 from fixtures.pageserver.utils import wait_until_tenant_active
+from fixtures.safekeeper.http import MembershipConfiguration, TimelineCreateRequest
 from fixtures.utils import query_scalar
 from performance.test_perf_pgbench import get_scales_matrix
 from requests import RequestException
@@ -164,6 +165,19 @@ def test_cannot_create_endpoint_on_non_uploaded_timeline(neon_env_builder: NeonE
     ps_http.configure_failpoints(("before-upload-index-pausable", "pause"))
     env.pageserver.tenant_create(env.initial_tenant)
 
+    sk = env.safekeepers[0]
+    assert sk
+    sk.http_client().timeline_create(
+        TimelineCreateRequest(
+            env.initial_tenant,
+            env.initial_timeline,
+            MembershipConfiguration(generation=1, members=[sk.safekeeper_id()], new_members=None),
+            int(env.pg_version),
+            Lsn(0),
+            None,
+        )
+    )
+
     initial_branch = "initial_branch"
 
     def start_creating_timeline():
diff --git a/test_runner/regress/test_normal_work.py b/test_runner/regress/test_normal_work.py
index 44590ea4b9..3335cf686c 100644
--- a/test_runner/regress/test_normal_work.py
+++ b/test_runner/regress/test_normal_work.py
@@ -64,6 +64,11 @@ def test_normal_work(
     """
 
     neon_env_builder.num_safekeepers = num_safekeepers
+
+    if safekeeper_proto_version == 2:
+        neon_env_builder.storage_controller_config = {
+            "timelines_onto_safekeepers": False,
+        }
     env = neon_env_builder.init_start()
     pageserver_http = env.pageserver.http_client()
 
diff --git a/test_runner/regress/test_ondemand_download.py b/test_runner/regress/test_ondemand_download.py
index 2590a3fe9d..2b71662669 100644
--- a/test_runner/regress/test_ondemand_download.py
+++ b/test_runner/regress/test_ondemand_download.py
@@ -671,6 +671,12 @@ def test_layer_download_cancelled_by_config_location(neon_env_builder: NeonEnvBu
     """
     neon_env_builder.enable_pageserver_remote_storage(s3_storage())
 
+    # On the new mode, the test runs into a cancellation issue, i.e. the walproposer can't shut down
+    # as it is hang-waiting on the timeline_checkpoint call in WalIngest::new.
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
+
     # turn off background tasks so that they don't interfere with the downloads
     env = neon_env_builder.init_start(
         initial_tenant_conf={
diff --git a/test_runner/regress/test_storage_controller.py b/test_runner/regress/test_storage_controller.py
index 8f3aa010e3..74ba74645e 100644
--- a/test_runner/regress/test_storage_controller.py
+++ b/test_runner/regress/test_storage_controller.py
@@ -88,6 +88,12 @@ def test_storage_controller_smoke(
     neon_env_builder.control_plane_hooks_api = compute_reconfigure_listener.control_plane_hooks_api
     env = neon_env_builder.init_configs()
 
+    # These bubble up from safekeepers
+    for ps in env.pageservers:
+        ps.allowed_errors.extend(
+            [".*Timeline.* has been deleted.*", ".*Timeline.*was cancelled and cannot be used"]
+        )
+
     # Start services by hand so that we can skip a pageserver (this will start + register later)
     env.broker.start()
     env.storage_controller.start()
@@ -3455,7 +3461,7 @@ def test_safekeeper_deployment_time_update(neon_env_builder: NeonEnvBuilder):
 
     assert target.get_safekeeper(fake_id) is None
 
-    assert len(target.get_safekeepers()) == 0
+    start_sks = target.get_safekeepers()
 
     sk_0 = env.safekeepers[0]
 
@@ -3477,7 +3483,7 @@ def test_safekeeper_deployment_time_update(neon_env_builder: NeonEnvBuilder):
 
     inserted = target.get_safekeeper(fake_id)
     assert inserted is not None
-    assert target.get_safekeepers() == [inserted]
+    assert target.get_safekeepers() == start_sks + [inserted]
     assert eq_safekeeper_records(body, inserted)
 
     # error out if pk is changed (unexpected)
@@ -3489,7 +3495,7 @@ def test_safekeeper_deployment_time_update(neon_env_builder: NeonEnvBuilder):
     assert exc.value.status_code == 400
 
     inserted_again = target.get_safekeeper(fake_id)
-    assert target.get_safekeepers() == [inserted_again]
+    assert target.get_safekeepers() == start_sks + [inserted_again]
     assert inserted_again is not None
     assert eq_safekeeper_records(inserted, inserted_again)
 
@@ -3498,7 +3504,7 @@ def test_safekeeper_deployment_time_update(neon_env_builder: NeonEnvBuilder):
     body["version"] += 1
     target.on_safekeeper_deploy(fake_id, body)
     inserted_now = target.get_safekeeper(fake_id)
-    assert target.get_safekeepers() == [inserted_now]
+    assert target.get_safekeepers() == start_sks + [inserted_now]
     assert inserted_now is not None
 
     assert eq_safekeeper_records(body, inserted_now)
@@ -3507,7 +3513,7 @@ def test_safekeeper_deployment_time_update(neon_env_builder: NeonEnvBuilder):
     body["https_port"] = 123
     target.on_safekeeper_deploy(fake_id, body)
     inserted_now = target.get_safekeeper(fake_id)
-    assert target.get_safekeepers() == [inserted_now]
+    assert target.get_safekeepers() == start_sks + [inserted_now]
     assert inserted_now is not None
     assert eq_safekeeper_records(body, inserted_now)
     env.storage_controller.consistency_check()
@@ -3516,7 +3522,7 @@ def test_safekeeper_deployment_time_update(neon_env_builder: NeonEnvBuilder):
     body["https_port"] = None
     target.on_safekeeper_deploy(fake_id, body)
     inserted_now = target.get_safekeeper(fake_id)
-    assert target.get_safekeepers() == [inserted_now]
+    assert target.get_safekeepers() == start_sks + [inserted_now]
     assert inserted_now is not None
     assert eq_safekeeper_records(body, inserted_now)
     env.storage_controller.consistency_check()
@@ -3635,6 +3641,9 @@ def test_timeline_delete_mid_live_migration(neon_env_builder: NeonEnvBuilder, mi
     env = neon_env_builder.init_configs()
     env.start()
 
+    for ps in env.pageservers:
+        ps.allowed_errors.append(".*Timeline.* has been deleted.*")
+
     tenant_id = TenantId.generate()
     timeline_id = TimelineId.generate()
     env.storage_controller.tenant_create(tenant_id, placement_policy={"Attached": 1})
diff --git a/test_runner/regress/test_storage_scrubber.py b/test_runner/regress/test_storage_scrubber.py
index 03cd133ccb..e29cb801d5 100644
--- a/test_runner/regress/test_storage_scrubber.py
+++ b/test_runner/regress/test_storage_scrubber.py
@@ -341,6 +341,11 @@ def test_scrubber_physical_gc_timeline_deletion(neon_env_builder: NeonEnvBuilder
     env = neon_env_builder.init_configs()
     env.start()
 
+    for ps in env.pageservers:
+        ps.allowed_errors.extend(
+            [".*Timeline.* has been deleted.*", ".*Timeline.*was cancelled and cannot be used"]
+        )
+
     tenant_id = TenantId.generate()
     timeline_id = TimelineId.generate()
     env.create_tenant(
diff --git a/test_runner/regress/test_timeline_detach_ancestor.py b/test_runner/regress/test_timeline_detach_ancestor.py
index f0810270b1..c58f78aeb1 100644
--- a/test_runner/regress/test_timeline_detach_ancestor.py
+++ b/test_runner/regress/test_timeline_detach_ancestor.py
@@ -21,7 +21,10 @@ from fixtures.neon_fixtures import (
     last_flush_lsn_upload,
     wait_for_last_flush_lsn,
 )
-from fixtures.pageserver.http import HistoricLayerInfo, PageserverApiException
+from fixtures.pageserver.http import (
+    HistoricLayerInfo,
+    PageserverApiException,
+)
 from fixtures.pageserver.utils import wait_for_last_record_lsn, wait_timeline_detail_404
 from fixtures.remote_storage import LocalFsStorage, RemoteStorageKind
 from fixtures.utils import assert_pageserver_backups_equal, skip_in_debug_build, wait_until
@@ -413,6 +416,7 @@ def test_ancestor_detach_behavior_v2(neon_env_builder: NeonEnvBuilder, snapshots
             "read_only": True,
         },
     )
+
     sk = env.safekeepers[0]
     assert sk
     with pytest.raises(requests.exceptions.HTTPError, match="Not Found"):
@@ -504,8 +508,15 @@ def test_ancestor_detach_behavior_v2(neon_env_builder: NeonEnvBuilder, snapshots
             assert len(lineage.get("original_ancestor", [])) == 0
             assert len(lineage.get("reparenting_history", [])) == 0
 
-    for name, _, _, rows, starts in expected_result:
-        with env.endpoints.create_start(name, tenant_id=env.initial_tenant) as ep:
+    for branch_name, queried_timeline, _, rows, starts in expected_result:
+        details = client.timeline_detail(env.initial_tenant, queried_timeline)
+        log.info(f"reading data from branch {branch_name}")
+        # specifying the lsn makes the endpoint read-only and not connect to safekeepers
+        with env.endpoints.create(
+            branch_name,
+            lsn=Lsn(details["last_record_lsn"]),
+        ) as ep:
+            ep.start(safekeeper_generation=1)
             assert ep.safe_psql("SELECT count(*) FROM foo;")[0][0] == rows
             assert ep.safe_psql(f"SELECT count(*) FROM audit WHERE starts = {starts}")[0][0] == 1
 
@@ -1088,6 +1099,7 @@ def test_timeline_detach_ancestor_interrupted_by_deletion(
 
     for ps in env.pageservers:
         ps.allowed_errors.extend(SHUTDOWN_ALLOWED_ERRORS)
+        ps.allowed_errors.append(".*Timeline.* has been deleted.*")
 
     pageservers = dict((int(p.id), p) for p in env.pageservers)
 
@@ -1209,6 +1221,7 @@ def test_sharded_tad_interleaved_after_partial_success(neon_env_builder: NeonEnv
 
     for ps in env.pageservers:
         ps.allowed_errors.extend(SHUTDOWN_ALLOWED_ERRORS)
+        ps.allowed_errors.append(".*Timeline.* has been deleted.*")
 
     pageservers = dict((int(p.id), p) for p in env.pageservers)
 
diff --git a/test_runner/regress/test_timeline_gc_blocking.py b/test_runner/regress/test_timeline_gc_blocking.py
index 9a710f5b80..8ef64a0742 100644
--- a/test_runner/regress/test_timeline_gc_blocking.py
+++ b/test_runner/regress/test_timeline_gc_blocking.py
@@ -24,6 +24,8 @@ def test_gc_blocking_by_timeline(neon_env_builder: NeonEnvBuilder, sharded: bool
         initial_tenant_conf={"gc_period": "1s", "lsn_lease_length": "0s"},
         initial_tenant_shard_count=2 if sharded else None,
     )
+    for ps in env.pageservers:
+        ps.allowed_errors.append(".*Timeline.* has been deleted.*")
 
     if sharded:
         http = env.storage_controller.pageserver_api()
diff --git a/test_runner/regress/test_wal_acceptor.py b/test_runner/regress/test_wal_acceptor.py
index b9183286af..ea120c1814 100644
--- a/test_runner/regress/test_wal_acceptor.py
+++ b/test_runner/regress/test_wal_acceptor.py
@@ -229,7 +229,7 @@ def test_many_timelines(neon_env_builder: NeonEnvBuilder):
 
     # Test timeline_list endpoint.
     http_cli = env.safekeepers[0].http_client()
-    assert len(http_cli.timeline_list()) == 3
+    assert len(http_cli.timeline_list()) == 4
 
 
 # Check that dead minority doesn't prevent the commits: execute insert n_inserts
@@ -740,8 +740,8 @@ def test_timeline_status(neon_env_builder: NeonEnvBuilder, auth_enabled: bool):
     env = neon_env_builder.init_start()
 
     tenant_id = env.initial_tenant
-    timeline_id = env.create_branch("test_timeline_status")
-    endpoint = env.endpoints.create_start("test_timeline_status")
+    timeline_id = env.initial_timeline
+    endpoint = env.endpoints.create_start("main")
 
     wa = env.safekeepers[0]
 
@@ -1292,6 +1292,12 @@ def test_lagging_sk(neon_env_builder: NeonEnvBuilder):
 # it works without compute at all.
 def test_peer_recovery(neon_env_builder: NeonEnvBuilder):
     neon_env_builder.num_safekeepers = 3
+
+    # timelines should be created the old way
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
+
     env = neon_env_builder.init_start()
 
     tenant_id = env.initial_tenant
@@ -1532,6 +1538,11 @@ def test_safekeeper_without_pageserver(
 
 
 def test_replace_safekeeper(neon_env_builder: NeonEnvBuilder):
+    # timelines should be created the old way manually until we have migration support
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
+
     def execute_payload(endpoint: Endpoint):
         with closing(endpoint.connect()) as conn:
             with conn.cursor() as cur:
@@ -1661,6 +1672,15 @@ def test_pull_timeline(neon_env_builder: NeonEnvBuilder, live_sk_change: bool):
     res = env.safekeepers[3].pull_timeline(
         [env.safekeepers[0], env.safekeepers[2]], tenant_id, timeline_id
     )
+    sk_id_1 = env.safekeepers[0].safekeeper_id()
+    sk_id_3 = env.safekeepers[2].safekeeper_id()
+    sk_id_4 = env.safekeepers[3].safekeeper_id()
+    new_conf = MembershipConfiguration(
+        generation=2, members=[sk_id_1, sk_id_3, sk_id_4], new_members=None
+    )
+    for i in [0, 2, 3]:
+        env.safekeepers[i].http_client().membership_switch(tenant_id, timeline_id, new_conf)
+
     log.info("Finished pulling timeline")
     log.info(res)
 
@@ -1705,13 +1725,15 @@ def test_pull_timeline_gc(neon_env_builder: NeonEnvBuilder):
     neon_env_builder.num_safekeepers = 3
     neon_env_builder.enable_safekeeper_remote_storage(default_remote_storage())
     env = neon_env_builder.init_start()
-    tenant_id = env.initial_tenant
-    timeline_id = env.initial_timeline
 
     (src_sk, dst_sk) = (env.safekeepers[0], env.safekeepers[2])
 
+    dst_sk.stop()
+
+    [tenant_id, timeline_id] = env.create_tenant()
+
     log.info("use only first 2 safekeepers, 3rd will be seeded")
-    endpoint = env.endpoints.create("main")
+    endpoint = env.endpoints.create("main", tenant_id=tenant_id)
     endpoint.active_safekeepers = [1, 2]
     endpoint.start()
     endpoint.safe_psql("create table t(key int, value text)")
@@ -1723,6 +1745,7 @@ def test_pull_timeline_gc(neon_env_builder: NeonEnvBuilder):
     src_http = src_sk.http_client()
     # run pull_timeline which will halt before downloading files
     src_http.configure_failpoints(("sk-snapshot-after-list-pausable", "pause"))
+    dst_sk.start()
     pt_handle = PropagatingThread(
         target=dst_sk.pull_timeline, args=([src_sk], tenant_id, timeline_id)
     )
@@ -1782,23 +1805,27 @@ def test_pull_timeline_term_change(neon_env_builder: NeonEnvBuilder):
     neon_env_builder.enable_safekeeper_remote_storage(default_remote_storage())
     env = neon_env_builder.init_start()
     tenant_id = env.initial_tenant
-    timeline_id = env.initial_timeline
 
     (src_sk, dst_sk) = (env.safekeepers[0], env.safekeepers[2])
+    dst_sk.stop()
 
+    src_http = src_sk.http_client()
+    src_http.configure_failpoints(("sk-snapshot-after-list-pausable", "pause"))
+
+    timeline_id = env.create_branch("pull_timeline_term_changes")
+
+    # run pull_timeline which will halt before downloading files
     log.info("use only first 2 safekeepers, 3rd will be seeded")
-    ep = env.endpoints.create("main")
+    ep = env.endpoints.create("pull_timeline_term_changes")
     ep.active_safekeepers = [1, 2]
     ep.start()
     ep.safe_psql("create table t(key int, value text)")
     ep.safe_psql("insert into t select generate_series(1, 1000), 'pear'")
 
-    src_http = src_sk.http_client()
-    # run pull_timeline which will halt before downloading files
-    src_http.configure_failpoints(("sk-snapshot-after-list-pausable", "pause"))
     pt_handle = PropagatingThread(
         target=dst_sk.pull_timeline, args=([src_sk], tenant_id, timeline_id)
     )
+    dst_sk.start()
     pt_handle.start()
     src_sk.wait_until_paused("sk-snapshot-after-list-pausable")
 
@@ -1807,7 +1834,7 @@ def test_pull_timeline_term_change(neon_env_builder: NeonEnvBuilder):
 
     # restart compute to bump term
     ep.stop()
-    ep = env.endpoints.create("main")
+    ep = env.endpoints.create("pull_timeline_term_changes")
     ep.active_safekeepers = [1, 2]
     ep.start()
     ep.safe_psql("insert into t select generate_series(1, 100), 'pear'")
@@ -1929,6 +1956,11 @@ def test_pull_timeline_while_evicted(neon_env_builder: NeonEnvBuilder):
 @run_only_on_default_postgres("tests only safekeeper API")
 def test_membership_api(neon_env_builder: NeonEnvBuilder):
     neon_env_builder.num_safekeepers = 1
+    # timelines should be created the old way
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
+
     env = neon_env_builder.init_start()
 
     # These are expected after timeline deletion on safekeepers.
@@ -2009,6 +2041,12 @@ def test_explicit_timeline_creation(neon_env_builder: NeonEnvBuilder):
     created manually, later storcon will do that.
     """
     neon_env_builder.num_safekeepers = 3
+
+    # timelines should be created the old way manually
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
+
     env = neon_env_builder.init_start()
 
     tenant_id = env.initial_tenant
@@ -2064,7 +2102,7 @@ def test_idle_reconnections(neon_env_builder: NeonEnvBuilder):
     env = neon_env_builder.init_start()
 
     tenant_id = env.initial_tenant
-    timeline_id = env.create_branch("test_idle_reconnections")
+    timeline_id = env.initial_timeline
 
     def collect_stats() -> dict[str, float]:
         # we need to collect safekeeper_pg_queries_received_total metric from all safekeepers
@@ -2095,7 +2133,7 @@ def test_idle_reconnections(neon_env_builder: NeonEnvBuilder):
 
     collect_stats()
 
-    endpoint = env.endpoints.create_start("test_idle_reconnections")
+    endpoint = env.endpoints.create_start("main")
     # just write something to the timeline
     endpoint.safe_psql("create table t(i int)")
     collect_stats()
diff --git a/test_runner/regress/test_wal_acceptor_async.py b/test_runner/regress/test_wal_acceptor_async.py
index d8a7dc2a2b..1bad387a90 100644
--- a/test_runner/regress/test_wal_acceptor_async.py
+++ b/test_runner/regress/test_wal_acceptor_async.py
@@ -590,6 +590,13 @@ async def run_wal_truncation(env: NeonEnv, safekeeper_proto_version: int):
 @pytest.mark.parametrize("safekeeper_proto_version", [2, 3])
 def test_wal_truncation(neon_env_builder: NeonEnvBuilder, safekeeper_proto_version: int):
     neon_env_builder.num_safekeepers = 3
+    if safekeeper_proto_version == 2:
+        # On the legacy protocol, we don't support generations, which are part of
+        # `timelines_onto_safekeepers`
+        neon_env_builder.storage_controller_config = {
+            "timelines_onto_safekeepers": False,
+        }
+
     env = neon_env_builder.init_start()
 
     asyncio.run(run_wal_truncation(env, safekeeper_proto_version))
@@ -713,6 +720,11 @@ async def run_quorum_sanity(env: NeonEnv):
 # we don't.
 def test_quorum_sanity(neon_env_builder: NeonEnvBuilder):
     neon_env_builder.num_safekeepers = 4
+
+    # The test fails basically always on the new mode.
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
     env = neon_env_builder.init_start()
 
     asyncio.run(run_quorum_sanity(env))
diff --git a/test_runner/regress/test_wal_receiver.py b/test_runner/regress/test_wal_receiver.py
index 0252b590cc..d281c055b0 100644
--- a/test_runner/regress/test_wal_receiver.py
+++ b/test_runner/regress/test_wal_receiver.py
@@ -16,6 +16,13 @@ if TYPE_CHECKING:
 # Checks that pageserver's walreceiver state is printed in the logs during WAL wait timeout.
 # Ensures that walreceiver does not run without any data inserted and only starts after the insertion.
 def test_pageserver_lsn_wait_error_start(neon_env_builder: NeonEnvBuilder):
+    # we assert below that the walreceiver is not active before data writes.
+    # with manually created timelines, it is active.
+    # FIXME: remove this test once we remove timelines_onto_safekeepers
+    neon_env_builder.storage_controller_config = {
+        "timelines_onto_safekeepers": False,
+    }
+
     # Trigger WAL wait timeout faster
     neon_env_builder.pageserver_config_override = "wait_lsn_timeout = '1s'"
     env = neon_env_builder.init_start()