diff --git a/tests/tui_gateway/test_checkpoints_config_fallback.py b/tests/tui_gateway/test_checkpoints_config_fallback.py
new file mode 100644
index 0000000000..8e4a0698e0
--- /dev/null
+++ b/tests/tui_gateway/test_checkpoints_config_fallback.py
@@ -0,0 +1,145 @@
+"""Tests for TUI/desktop checkpoint config fallback (#79625).
+
+Desktop sessions (via ``hermes serve`` → TUI gateway) never set
+``HERMES_TUI_CHECKPOINTS``, so agent creation gated filesystem checkpoints
+on that env var alone — ``checkpoints.enabled: true`` in config.yaml was
+silently ignored on the desktop surface while the CLI and messaging gateway
+honored it. The fix makes ``_make_agent`` fall back to the ``checkpoints``
+config section when the env var is unset, mirroring the messaging gateway's
+``_checkpoint_agent_kwargs`` (gateway/run.py).
+"""
+
+import os
+
+import pytest
+
+from tui_gateway import server
+
+
+class TestLoadCheckpointsEnabled:
+    def test_defaults_to_false_when_no_config_section(self):
+        """No ``checkpoints`` section → DEFAULT_CONFIG default (disabled)."""
+        assert server._load_checkpoints_enabled({}) is False
+
+    def test_honors_config_enabled_true(self):
+        """``checkpoints: {enabled: true}`` in config.yaml enables checkpoints."""
+        assert server._load_checkpoints_enabled({"checkpoints": {"enabled": True}}) is True
+
+    def test_honors_config_enabled_false(self):
+        assert server._load_checkpoints_enabled({"checkpoints": {"enabled": False}}) is False
+
+    def test_legacy_bool_form(self):
+        """Legacy ``checkpoints: true`` (bare bool) still enables."""
+        assert server._load_checkpoints_enabled({"checkpoints": True}) is True
+        assert server._load_checkpoints_enabled({"checkpoints": False}) is False
+
+    def test_malformed_section_falls_back_to_default(self):
+        assert server._load_checkpoints_enabled({"checkpoints": "enabled"}) is False
+
+    def test_none_cfg_falls_back(self):
+        assert server._load_checkpoints_enabled(None) is False
+
+
+class TestResolveCheckpointsEnabled:
+    """The env-var-first precedence used by ``_make_agent``."""
+
+    def test_config_enabled_used_when_env_unset(self, monkeypatch):
+        """Desktop path: no HERMES_TUI_CHECKPOINTS → config ``enabled: true`` wins."""
+        monkeypatch.delenv("HERMES_TUI_CHECKPOINTS", raising=False)
+        assert server._resolve_checkpoints_enabled(
+            {"checkpoints": {"enabled": True}}
+        ) is True
+
+    def test_config_disabled_used_when_env_unset(self, monkeypatch):
+        monkeypatch.delenv("HERMES_TUI_CHECKPOINTS", raising=False)
+        assert server._resolve_checkpoints_enabled(
+            {"checkpoints": {"enabled": False}}
+        ) is False
+
+    def test_env_var_overrides_config(self, monkeypatch):
+        """CLI ``--tui --checkpoints`` (env set) still wins over config."""
+        monkeypatch.setenv("HERMES_TUI_CHECKPOINTS", "1")
+        assert server._resolve_checkpoints_enabled(
+            {"checkpoints": {"enabled": False}}
+        ) is True
+
+    def test_env_var_false_overrides_config_true(self, monkeypatch):
+        monkeypatch.setenv("HERMES_TUI_CHECKPOINTS", "0")
+        assert server._resolve_checkpoints_enabled(
+            {"checkpoints": {"enabled": True}}
+        ) is False
+
+
+class TestMakeAgentCheckpointsFallback:
+    """The env-var → config fallback inside ``_make_agent`` (the wiring).
+
+    Addresses review: unit tests of the helper alone could false-pass if
+    ``_make_agent`` never actually passed the value through. These drive
+    ``_make_agent`` end-to-end with a fake ``AIAgent`` that captures
+    kwargs, proving the config-derived value reaches the agent.
+    """
+
+    def _make_agent_with_checkpoints(self, monkeypatch, cfg, env_val="__unset__"):
+        import types
+
+        captured = {}
+
+        def fake_agent(**kwargs):
+            captured.update(kwargs)
+            return types.SimpleNamespace(model=kwargs.get("model"))
+
+        if env_val == "__unset__":
+            monkeypatch.delenv("HERMES_TUI_CHECKPOINTS", raising=False)
+        else:
+            monkeypatch.setenv("HERMES_TUI_CHECKPOINTS", env_val)
+        monkeypatch.delenv("HERMES_MODEL", raising=False)
+        monkeypatch.delenv("HERMES_INFERENCE_MODEL", raising=False)
+        monkeypatch.delenv("HERMES_TUI_PROVIDER", raising=False)
+        monkeypatch.delenv("HERMES_DESKTOP", raising=False)
+        monkeypatch.delenv("HERMES_DESKTOP_TERMINAL", raising=False)
+        monkeypatch.setattr(
+            server, "_load_cfg",
+            lambda: {**cfg, "model": {"default": "gpt-5.5", "provider": "openai-codex"}},
+        )
+        monkeypatch.setattr(
+            "hermes_cli.runtime_provider.resolve_runtime_provider",
+            lambda requested=None, target_model=None: {
+                "provider": "openai-codex",
+                "base_url": "https://chatgpt.com/backend-api/codex",
+                "api_key": "token",
+                "api_mode": "codex_responses",
+                "credential_pool": None,
+            },
+        )
+        monkeypatch.setattr("run_agent.AIAgent", fake_agent)
+        monkeypatch.setattr(server, "_load_enabled_toolsets", lambda platform=None: ["file"])
+        monkeypatch.setattr(server, "_get_db", lambda: None)
+        server._make_agent("sid", "session-key")
+        return captured
+
+    def test_desktop_config_enabled_reaches_agent(self, monkeypatch):
+        """Issue #79625: config ``enabled: true`` (env unset) → agent has
+        checkpoints_enabled=True. On the old code this was always False."""
+        captured = self._make_agent_with_checkpoints(
+            monkeypatch, {"checkpoints": {"enabled": True}}
+        )
+        assert captured.get("checkpoints_enabled") is True
+
+    def test_desktop_config_disabled_reaches_agent(self, monkeypatch):
+        captured = self._make_agent_with_checkpoints(
+            monkeypatch, {"checkpoints": {"enabled": False}}
+        )
+        assert captured.get("checkpoints_enabled") is False
+
+    def test_cli_env_override_still_wins(self, monkeypatch):
+        """Legacy ``--tui --checkpoints`` (env '1') overrides config False."""
+        captured = self._make_agent_with_checkpoints(
+            monkeypatch, {"checkpoints": {"enabled": False}}, env_val="1"
+        )
+        assert captured.get("checkpoints_enabled") is True
+
+    def test_cli_env_off_still_wins(self, monkeypatch):
+        captured = self._make_agent_with_checkpoints(
+            monkeypatch, {"checkpoints": {"enabled": True}}, env_val="0"
+        )
+        assert captured.get("checkpoints_enabled") is False
diff --git a/tui_gateway/checkpoints.py b/tui_gateway/checkpoints.py
new file mode 100644
index 0000000000..642d3665d6
--- /dev/null
+++ b/tui_gateway/checkpoints.py
@@ -0,0 +1,55 @@
+"""Checkpoint-enablement resolution for TUI-created agents (issue #79625).
+
+Desktop sessions (``hermes serve`` → TUI gateway) never set ``HERMES_TUI_CHECKPOINTS``
+(that env var is only set by the ``hermes --tui --checkpoints`` CLI path), so agent
+creation previously gated filesystem checkpointing on the env var alone and silently
+ignored ``checkpoints.enabled`` in config.yaml. These helpers resolve enablement the
+way the messaging gateway does (``gateway/run.py`` ``_checkpoint_agent_kwargs``):
+the env var (explicit CLI opt-in) wins when set, otherwise the ``checkpoints``
+config section applies with ``DEFAULT_CONFIG`` defaults.
+"""
+
+import os
+
+from utils import is_truthy_value
+
+
+def _load_checkpoints_enabled(cfg: dict | None = None) -> bool:
+    """Whether filesystem checkpoints are enabled for TUI-created agents.
+
+    Keeps the legacy ``checkpoints: true`` bool form working and falls back to the
+    ``DEFAULT_CONFIG`` default when the section is absent or malformed.
+    """
+    cp_cfg = (cfg or {}).get("checkpoints", {})
+    if isinstance(cp_cfg, bool):
+        cp_cfg = {"enabled": cp_cfg}
+    elif not isinstance(cp_cfg, dict):
+        cp_cfg = {}
+    from hermes_cli.config import DEFAULT_CONFIG
+    return bool(cp_cfg.get("enabled", DEFAULT_CONFIG["checkpoints"]["enabled"]))
+
+
+def resolve_checkpoints_enabled(cfg: dict | None = None) -> bool:
+    """Resolve checkpoint enablement with the env-var override first.
+
+    ``HERMES_TUI_CHECKPOINTS`` (set by ``hermes --tui --checkpoints``) is the
+    explicit opt-in and wins when present; otherwise fall back to the
+    ``checkpoints`` config section (issue #79625 — the desktop backend never
+    sets the env var, so config was being silently ignored).
+    """
+    env_val = os.environ.get("HERMES_TUI_CHECKPOINTS")
+    if env_val is not None:
+        return is_truthy_value(env_val)
+    return _load_checkpoints_enabled(cfg)
+
+
+def _resolve_checkpoint_hash(mgr, cwd: str, ref: str) -> str:
+    """``/rollback N`` style number → the checkpoint's hash; a real hash passes through."""
+    try:
+        checkpoints = mgr.list_checkpoints(cwd)
+        idx = int(ref) - 1
+    except ValueError:
+        return ref
+    if 0 <= idx < len(checkpoints):
+        return checkpoints[idx].get("hash", ref)
+    raise ValueError(f"Invalid checkpoint number. Use 1-{len(checkpoints)}.")
diff --git a/tui_gateway/server.py b/tui_gateway/server.py
index 2ec14e2952..641f2221af 100644
--- a/tui_gateway/server.py
+++ b/tui_gateway/server.py
@@ -37,6 +37,8 @@ from agent.compaction_display import project_compaction_message_for_display  # n
 from agent.skill_commands import describe_skill_invocation  # noqa: F401
 from agent.conversation_loop import INTERRUPT_WAITING_FOR_MODEL_PREFIX  # noqa: F401
 from tui_gateway import git_probe
+from tui_gateway.checkpoints import (_load_checkpoints_enabled, _resolve_checkpoint_hash,
+                                     resolve_checkpoints_enabled as _resolve_checkpoints_enabled)  # noqa: F401
 from tui_gateway._env import env_float, env_int
 from tui_gateway.turn_marker import clear_turn_marker, marker_writer_state, read_turn_marker, record_turn_start  # noqa: F401
 from tui_gateway.contracts import registry as _contracts
@@ -2683,7 +2685,7 @@ def _make_agent(
         # Builds that run before the record exists (branch, eager resume, compute host) pass it explicitly.
         user_id=auth_user_id if auth_user_id is not None else _session_auth_user_id(session),
         session_db=session_db if session_db is not None else _get_db(), ephemeral_system_prompt=system_prompt or None,
-        checkpoints_enabled=is_truthy_value(os.environ.get("HERMES_TUI_CHECKPOINTS")),
+        checkpoints_enabled=_resolve_checkpoints_enabled(cfg),
         pass_session_id=is_truthy_value(os.environ.get("HERMES_TUI_PASS_SESSION_ID")),
         skip_context_files=ignore_rules, skip_memory=ignore_rules, fallback_model=_load_fallback_model(),
         # The resolved provider's request body (a custom entry's extra_body), as the CLI/cron/gateway pass it.
@@ -2814,17 +2816,6 @@ def _with_checkpoints(session, fn):
     return fn(session["agent"]._checkpoint_mgr, _session_cwd(session))
 
 
-def _resolve_checkpoint_hash(mgr, cwd: str, ref: str) -> str:
-    try:
-        checkpoints = mgr.list_checkpoints(cwd)
-        idx = int(ref) - 1
-    except ValueError:
-        return ref
-    if 0 <= idx < len(checkpoints):
-        return checkpoints[idx].get("hash", ref)
-    raise ValueError(f"Invalid checkpoint number. Use 1-{len(checkpoints)}.")
-
-
 # ── Methods: session ─────────────────────────────────────────────────