diff --git a/changelog.d/fix-invalidate-caches-perf.fixed.md b/changelog.d/fix-invalidate-caches-perf.fixed.md
new file mode 100644
index 00000000..d1828b78
--- /dev/null
+++ b/changelog.d/fix-invalidate-caches-perf.fixed.md
@@ -0,0 +1 @@
+Iterate only existing holders in `_invalidate_all_caches`. The 3.24.4-era implementation walked every variable in the tax-benefit system and lazy-created a `Holder` for each one, inflating `apply_reform` from milliseconds to seconds in downstream packages with thousands of variables (policyengine-us YAML full-suite went from ~17 min to ~51 min per job and started timing out at the 1-hour GitHub Actions limit). Untouched variables have no holder and therefore nothing to wipe, so iterating `population._holders.values()` on each population recovers the original performance while keeping the set_input preservation behaviour introduced in #475.
diff --git a/policyengine_core/simulations/simulation.py b/policyengine_core/simulations/simulation.py
index a7916c29..6b5f1118 100644
--- a/policyengine_core/simulations/simulation.py
+++ b/policyengine_core/simulations/simulation.py
@@ -283,14 +283,17 @@ def _invalidate_all_caches(self) -> None:
             stored_value = holder._memory_storage._arrays.get(storage_key)
             if stored_value is not None:
                 preserved.setdefault(variable_name, {})[storage_key] = stored_value
-        for variable in list(self.tax_benefit_system.variables):
-            holder = self.get_holder(variable)
-            # Wipe formula outputs and on-disk caches on both memory and
-            # disk storage. After the storage-delete bug fix (C2) that
-            # respects branch_name, so wipe both.
-            holder._memory_storage._arrays = {}
-            if holder._disk_storage is not None:
-                holder._disk_storage._files = {}
+        # Iterate only over holders that already exist on each population —
+        # lazy-creating a holder for every variable in the tax-benefit
+        # system (thousands in policyengine-us) inflated the cost of
+        # ``apply_reform`` from milliseconds to seconds and broke the
+        # YAML full-suite on downstream repos. Untouched variables have
+        # no holder and therefore nothing to wipe.
+        for population in self.populations.values():
+            for holder in population._holders.values():
+                holder._memory_storage._arrays = {}
+                if holder._disk_storage is not None:
+                    holder._disk_storage._files = {}
         # Replay preserved user inputs so ``calculate`` still sees them.
         for variable_name, key_to_array in preserved.items():
             holder = self.get_holder(variable_name)
diff --git a/uv.lock b/uv.lock
index 16ec94e9..b2d11c3e 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2384,7 +2384,7 @@ wheels = [
 
 [[package]]
 name = "policyengine-core"
-version = "3.24.4"
+version = "3.25.0"
 source = { editable = "." }
 dependencies = [
     { name = "dpath" },