diff --git a/activitysim/abm/models/joint_tour_frequency_composition.py b/activitysim/abm/models/joint_tour_frequency_composition.py
index 1fffd892a..cc7f82c0d 100644
--- a/activitysim/abm/models/joint_tour_frequency_composition.py
+++ b/activitysim/abm/models/joint_tour_frequency_composition.py
@@ -44,11 +44,9 @@ def joint_tour_frequency_composition(
             model_settings_file_name,
         )
 
-    # FIXME setting index as "alt" causes crash in estimation mode...
     alts = simulate.read_model_alts(
-        state, "joint_tour_frequency_composition_alternatives.csv", set_index=None
+        state, "joint_tour_frequency_composition_alternatives.csv", set_index="alt"
     )
-    alts.index = alts["alt"].values
 
     # - only interested in households with more than one cdap travel_active person and
     # - at least one non-preschooler
diff --git a/activitysim/abm/models/school_escorting.py b/activitysim/abm/models/school_escorting.py
index 32e5058e7..491d0ac0c 100644
--- a/activitysim/abm/models/school_escorting.py
+++ b/activitysim/abm/models/school_escorting.py
@@ -308,7 +308,7 @@ def create_school_escorting_bundles_table(choosers, tours, stage):
         bundles["chauf_id"],
     )
 
-    bundles["Alt"] = choosers["Alt"]
+    bundles["alt"] = choosers["alt"]
     bundles["Description"] = choosers["Description"]
 
     return bundles
@@ -412,11 +412,7 @@ def school_escorting(
 
     trace_hh_id = state.settings.trace_hh_id
 
-    # FIXME setting index as "Alt" causes crash in estimation mode...
-    # happens in joint_tour_frequency_composition too!
-    # alts = simulate.read_model_alts(state, model_settings.ALTS, set_index="Alt")
-    alts = simulate.read_model_alts(state, model_settings.ALTS, set_index=None)
-    alts.index = alts["Alt"].values
+    alts = simulate.read_model_alts(state, model_settings.ALTS, set_index="alt")
 
     choosers, participant_columns = determine_escorting_participants(
         households_merged, persons, model_settings
@@ -565,10 +561,10 @@ def school_escorting(
             )
 
         if stage_num >= 1:
-            choosers["Alt"] = choices
-            choosers = choosers.join(alts.set_index("Alt"), how="left", on="Alt")
+            choosers["alt"] = choices
+            choosers = choosers.join(alts, how="left", on="alt")
             bundles = create_school_escorting_bundles_table(
-                choosers[choosers["Alt"] > 1], tours, stage
+                choosers[choosers["alt"] > 1], tours, stage
             )
             escort_bundles.append(bundles)
 
diff --git a/activitysim/core/simulate.py b/activitysim/core/simulate.py
index 55caf050a..7ced099d9 100644
--- a/activitysim/core/simulate.py
+++ b/activitysim/core/simulate.py
@@ -79,7 +79,22 @@ def read_model_alts(state: workflow.State, file_name, set_index=None):
     file_path = state.filesystem.get_config_file_path(file_name)
     df = pd.read_csv(file_path, comment="#")
     if set_index:
+        if "Alt" in df.columns:
+            # Handle deprecated ALTS index
+            warnings.warn(
+                "Support for 'Alt' column name in alternatives files will be removed."
+                " Use 'alt' (lowercase) instead.",
+                DeprecationWarning,
+            )
+            # warning above does not actually output to logger, so also log it
+            logger.warning(
+                "Support for 'Alt' column name in alternatives files will be removed."
+                " Use 'alt' (lowercase) instead."
+            )
+            df.rename(columns={"Alt": "alt"}, inplace=True)
+
         df.set_index(set_index, inplace=True)
+
     return df
 
 
diff --git a/activitysim/examples/prototype_mtc_extended/test/prototype_mtc_extended_reference_pipeline.zip b/activitysim/examples/prototype_mtc_extended/test/prototype_mtc_extended_reference_pipeline.zip
index 41ed28ba2..9654facfb 100644
Binary files a/activitysim/examples/prototype_mtc_extended/test/prototype_mtc_extended_reference_pipeline.zip and b/activitysim/examples/prototype_mtc_extended/test/prototype_mtc_extended_reference_pipeline.zip differ
diff --git a/docs/dev-guide/changes.md b/docs/dev-guide/changes.md
index 2cd584b3c..b86a9d84c 100644
--- a/docs/dev-guide/changes.md
+++ b/docs/dev-guide/changes.md
@@ -13,6 +13,15 @@ branch (i.e., the main branch on GitHub), but not yet released in a stable versi
 of ActivitySim.  See below under the various version headings for changes in 
 released versions.
 
+## v1.5.2
+
+### Alternative file naming consistency
+
+We have enforced a naming scheme for alternative config files to have the index name
+be 'alt' instead of 'Alt'. This is to maintain consistency across all config files.
+The code will handle this for you, but you will get a deprecation warning if you
+are using 'Alt' in your config files. Please update your config files to use 'alt'.
+See ActivitySim issue [#846](https://github.com/ActivitySim/activitysim/issues/846)
 
 ## v1.5.1