diff --git a/source/blender/blenkernel/BKE_instances.hh b/source/blender/blenkernel/BKE_instances.hh
index 87d2fc3efcc..7bd81aa0e08 100644
--- a/source/blender/blenkernel/BKE_instances.hh
+++ b/source/blender/blenkernel/BKE_instances.hh
@@ -19,13 +19,13 @@
  * which is then stored per instance. Many instances can use the same #InstanceReference.
  */
 
-#include <mutex>
 #include <optional>
 
 #include "BLI_array.hh"
 #include "BLI_function_ref.hh"
 #include "BLI_index_mask_fwd.hh"
 #include "BLI_math_matrix_types.hh"
+#include "BLI_shared_cache.hh"
 #include "BLI_vector.hh"
 
 #include "DNA_customdata_types.h"
@@ -99,19 +99,16 @@ class Instances {
    */
   Vector<InstanceReference> references_;
 
-  /** Indices into `references_`. Determines what data is instanced. */
-  Vector<int> reference_handles_;
   /** Transformation of the instances. */
   Vector<float4x4> transforms_;
 
+  CustomData attributes_;
+
   /* These almost unique ids are generated based on the `id` attribute, which might not contain
    * unique ids at all. They are *almost* unique, because under certain very unlikely
    * circumstances, they are not unique. Code using these ids should not crash when they are not
    * unique but can generally expect them to be unique. */
-  mutable std::mutex almost_unique_ids_mutex_;
-  mutable Array<int> almost_unique_ids_;
-
-  CustomData attributes_;
+  mutable SharedCache<Array<int>> almost_unique_ids_cache_;
 
  public:
   Instances();
@@ -161,7 +158,7 @@ class Instances {
   GeometrySet &geometry_set_from_reference(int reference_index);
 
   Span<int> reference_handles() const;
-  MutableSpan<int> reference_handles();
+  MutableSpan<int> reference_handles_for_write();
   MutableSpan<float4x4> transforms();
   Span<float4x4> transforms() const;
 
@@ -189,6 +186,11 @@ class Instances {
 
   bool owns_direct_data() const;
   void ensure_owns_direct_data();
+
+  void tag_reference_handles_changed()
+  {
+    almost_unique_ids_cache_.tag_dirty();
+  }
 };
 
 /* -------------------------------------------------------------------- */
diff --git a/source/blender/blenkernel/intern/attribute_access.cc b/source/blender/blenkernel/intern/attribute_access.cc
index 163e20708df..92764d2df09 100644
--- a/source/blender/blenkernel/intern/attribute_access.cc
+++ b/source/blender/blenkernel/intern/attribute_access.cc
@@ -129,6 +129,9 @@ bool allow_procedural_attribute_access(StringRef attribute_name)
   if (attribute_name.startswith(".uv")) {
     return false;
   }
+  if (attribute_name == ".reference_index") {
+    return false;
+  }
   if (attribute_name.startswith("." UV_VERTSEL_NAME ".")) {
     return false;
   }
diff --git a/source/blender/blenkernel/intern/bake_items_serialize.cc b/source/blender/blenkernel/intern/bake_items_serialize.cc
index ea5b57b3677..28edca63a09 100644
--- a/source/blender/blenkernel/intern/bake_items_serialize.cc
+++ b/source/blender/blenkernel/intern/bake_items_serialize.cc
@@ -724,19 +724,25 @@ static std::unique_ptr<Instances> try_load_instances(const DictionaryValue &io_g
     return {};
   }
 
-  const auto *io_handles = io_instances->lookup_dict("handles");
-  if (!io_handles) {
-    return {};
-  }
-  if (!read_blob_simple_gspan(blob_reader, *io_handles, instances->reference_handles())) {
-    return {};
-  }
-
   MutableAttributeAccessor attributes = instances->attributes_for_write();
   if (!load_attributes(*io_attributes, attributes, blob_reader, blob_sharing)) {
     return {};
   }
 
+  if (!attributes.contains(".reference_index")) {
+    /* Try reading the reference index attribute from the old bake format from before it was an
+     * attribute. */
+    const auto *io_handles = io_instances->lookup_dict("handles");
+    if (!io_handles) {
+      return {};
+    }
+    if (!read_blob_simple_gspan(
+            blob_reader, *io_handles, instances->reference_handles_for_write()))
+    {
+      return {};
+    }
+  }
+
   return instances;
 }
 
@@ -969,9 +975,6 @@ static std::shared_ptr<DictionaryValue> serialize_geometry_set(const GeometrySet
 
     io_instances->append(
         "transforms", write_blob_simple_gspan(blob_writer, blob_sharing, instances.transforms()));
-    io_instances->append(
-        "handles",
-        write_blob_simple_gspan(blob_writer, blob_sharing, instances.reference_handles()));
 
     auto io_attributes = serialize_attributes(
         instances.attributes(), blob_writer, blob_sharing, {"position"});
diff --git a/source/blender/blenkernel/intern/geometry_component_instances.cc b/source/blender/blenkernel/intern/geometry_component_instances.cc
index 961705a19dc..a417f29faf4 100644
--- a/source/blender/blenkernel/intern/geometry_component_instances.cc
+++ b/source/blender/blenkernel/intern/geometry_component_instances.cc
@@ -168,6 +168,12 @@ class InstancePositionAttributeProvider final : public BuiltinAttributeProvider
   }
 };
 
+static void tag_component_reference_index_changed(void *owner)
+{
+  Instances &instances = *static_cast<Instances *>(owner);
+  instances.tag_reference_handles_changed();
+}
+
 static ComponentAttributeProviders create_attribute_providers_for_instances()
 {
   static InstancePositionAttributeProvider position;
@@ -200,10 +206,20 @@ static ComponentAttributeProviders create_attribute_providers_for_instances()
                                            instance_custom_data_access,
                                            nullptr);
 
+  /** Indices into `Instances::references_`. Determines what data is instanced. */
+  static BuiltinCustomDataLayerProvider reference_index(".reference_index",
+                                                        AttrDomain::Instance,
+                                                        CD_PROP_INT32,
+                                                        CD_PROP_INT32,
+                                                        BuiltinAttributeProvider::Creatable,
+                                                        BuiltinAttributeProvider::NonDeletable,
+                                                        instance_custom_data_access,
+                                                        tag_component_reference_index_changed);
+
   static CustomDataAttributeProvider instance_custom_data(AttrDomain::Instance,
                                                           instance_custom_data_access);
 
-  return ComponentAttributeProviders({&position, &id}, {&instance_custom_data});
+  return ComponentAttributeProviders({&position, &id, &reference_index}, {&instance_custom_data});
 }
 
 static AttributeAccessorFunctions get_instances_accessor_functions()
diff --git a/source/blender/blenkernel/intern/instances.cc b/source/blender/blenkernel/intern/instances.cc
index 2214bbe4da1..f43fba35002 100644
--- a/source/blender/blenkernel/intern/instances.cc
+++ b/source/blender/blenkernel/intern/instances.cc
@@ -51,19 +51,17 @@ Instances::Instances()
 
 Instances::Instances(Instances &&other)
     : references_(std::move(other.references_)),
-      reference_handles_(std::move(other.reference_handles_)),
       transforms_(std::move(other.transforms_)),
-      almost_unique_ids_(std::move(other.almost_unique_ids_)),
-      attributes_(other.attributes_)
+      attributes_(other.attributes_),
+      almost_unique_ids_cache_(std::move(other.almost_unique_ids_cache_))
 {
   CustomData_reset(&other.attributes_);
 }
 
 Instances::Instances(const Instances &other)
     : references_(other.references_),
-      reference_handles_(other.reference_handles_),
       transforms_(other.transforms_),
-      almost_unique_ids_(other.almost_unique_ids_)
+      almost_unique_ids_cache_(other.almost_unique_ids_cache_)
 {
   CustomData_copy(&other.attributes_, &attributes_, CD_MASK_ALL, other.instances_num());
 }
@@ -96,7 +94,6 @@ Instances &Instances::operator=(Instances &&other)
 void Instances::resize(int capacity)
 {
   const int old_size = this->instances_num();
-  reference_handles_.resize(capacity);
   transforms_.resize(capacity);
   CustomData_realloc(&attributes_, old_size, capacity, CD_SET_DEFAULT);
 }
@@ -106,19 +103,27 @@ void Instances::add_instance(const int instance_handle, const float4x4 &transfor
   BLI_assert(instance_handle >= 0);
   BLI_assert(instance_handle < references_.size());
   const int old_size = this->instances_num();
-  reference_handles_.append(instance_handle);
   transforms_.append(transform);
   CustomData_realloc(&attributes_, old_size, transforms_.size());
+  this->reference_handles_for_write().last() = instance_handle;
 }
 
 Span<int> Instances::reference_handles() const
 {
-  return reference_handles_;
+  return {static_cast<const int *>(
+              CustomData_get_layer_named(&attributes_, CD_PROP_INT32, ".reference_index")),
+          this->instances_num()};
 }
 
-MutableSpan<int> Instances::reference_handles()
+MutableSpan<int> Instances::reference_handles_for_write()
 {
-  return reference_handles_;
+  int *data = static_cast<int *>(CustomData_get_layer_named_for_write(
+      &attributes_, CD_PROP_INT32, ".reference_index", this->instances_num()));
+  if (!data) {
+    data = static_cast<int *>(CustomData_add_layer_named(
+        &attributes_, CD_PROP_INT32, CD_SET_DEFAULT, this->instances_num(), ".reference_index"));
+  }
+  return {data, this->instances_num()};
 }
 
 MutableSpan<float4x4> Instances::transforms()
@@ -178,10 +183,7 @@ void Instances::remove(const IndexMask &mask,
 
   Instances new_instances;
   new_instances.references_ = std::move(references_);
-  new_instances.reference_handles_.resize(new_size);
   new_instances.transforms_.resize(new_size);
-  array_utils::gather(
-      reference_handles_.as_span(), mask, new_instances.reference_handles_.as_mutable_span());
   array_utils::gather(transforms_.as_span(), mask, new_instances.transforms_.as_mutable_span());
 
   gather_attributes(this->attributes(),
@@ -212,6 +214,8 @@ void Instances::remove_unused_references()
     return;
   }
 
+  const Span<int> reference_handles = this->reference_handles();
+
   Array<bool> usage_by_handle(tot_references_before, false);
   std::mutex mutex;
 
@@ -221,7 +225,7 @@ void Instances::remove_unused_references()
     Array<bool> local_usage_by_handle(tot_references_before, false);
 
     for (const int i : range) {
-      const int handle = reference_handles_[i];
+      const int handle = reference_handles[i];
       BLI_assert(handle >= 0 && handle < tot_references_before);
       local_usage_by_handle[handle] = true;
     }
@@ -266,11 +270,14 @@ void Instances::remove_unused_references()
   }
 
   /* Update handles of instances. */
-  threading::parallel_for(IndexRange(tot_instances), 1000, [&](IndexRange range) {
-    for (const int i : range) {
-      reference_handles_[i] = handle_mapping[reference_handles_[i]];
-    }
-  });
+  {
+    const MutableSpan<int> reference_handles = this->reference_handles_for_write();
+    threading::parallel_for(IndexRange(tot_instances), 1000, [&](IndexRange range) {
+      for (const int i : range) {
+        reference_handles[i] = handle_mapping[reference_handles[i]];
+      }
+    });
+  }
 }
 
 int Instances::instances_num() const
@@ -357,21 +364,20 @@ static Array<int> generate_unique_instance_ids(Span<int> original_ids)
 
 Span<int> Instances::almost_unique_ids() const
 {
-  std::lock_guard lock(almost_unique_ids_mutex_);
-  bke::AttributeReader<int> instance_ids_attribute = this->attributes().lookup<int>("id");
-  if (instance_ids_attribute) {
-    Span<int> instance_ids = instance_ids_attribute.varray.get_internal_span();
-    if (almost_unique_ids_.size() != instance_ids.size()) {
-      almost_unique_ids_ = generate_unique_instance_ids(instance_ids);
+  almost_unique_ids_cache_.ensure([&](Array<int> &r_data) {
+    bke::AttributeReader<int> instance_ids_attribute = this->attributes().lookup<int>("id");
+    if (instance_ids_attribute) {
+      Span<int> instance_ids = instance_ids_attribute.varray.get_internal_span();
+      if (r_data.size() != instance_ids.size()) {
+        r_data = generate_unique_instance_ids(instance_ids);
+      }
     }
-  }
-  else {
-    almost_unique_ids_.reinitialize(this->instances_num());
-    for (const int i : almost_unique_ids_.index_range()) {
-      almost_unique_ids_[i] = i;
+    else {
+      r_data.reinitialize(this->instances_num());
+      array_utils::fill_index_range(r_data.as_mutable_span());
     }
-  }
-  return almost_unique_ids_;
+  });
+  return almost_unique_ids_cache_.data();
 }
 
 }  // namespace blender::bke
diff --git a/source/blender/geometry/intern/join_geometries.cc b/source/blender/geometry/intern/join_geometries.cc
index 3cc6175db0a..2acaf0d8909 100644
--- a/source/blender/geometry/intern/join_geometries.cc
+++ b/source/blender/geometry/intern/join_geometries.cc
@@ -110,7 +110,7 @@ static void join_instances(const Span<const GeometryComponent *> src_components,
   dst_instances->resize(offsets.total_size());
 
   MutableSpan<float4x4> all_transforms = dst_instances->transforms();
-  MutableSpan<int> all_handles = dst_instances->reference_handles();
+  MutableSpan<int> all_handles = dst_instances->reference_handles_for_write();
 
   for (const int i : src_components.index_range()) {
     const auto &src_component = static_cast<const bke::InstancesComponent &>(*src_components[i]);
@@ -131,7 +131,7 @@ static void join_instances(const Span<const GeometryComponent *> src_components,
 
   result.replace_instances(dst_instances.release());
   auto &dst_component = result.get_component_for_write<bke::InstancesComponent>();
-  join_attributes(src_components, dst_component, {"position"});
+  join_attributes(src_components, dst_component, {"position", ".reference_index"});
 }
 
 static void join_volumes(const Span<const GeometryComponent *> /*src_components*/,
diff --git a/source/blender/geometry/intern/randomize.cc b/source/blender/geometry/intern/randomize.cc
index f61c5af74bc..77a516b806c 100644
--- a/source/blender/geometry/intern/randomize.cc
+++ b/source/blender/geometry/intern/randomize.cc
@@ -253,7 +253,7 @@ void debug_randomize_instance_order(bke::Instances *instances)
     new_transforms[new_i] = old_transforms[old_i];
   }
 
-  instances->reference_handles().copy_from(new_reference_handles);
+  instances->reference_handles_for_write().copy_from(new_reference_handles);
   instances->transforms().copy_from(new_transforms);
 }
 
diff --git a/source/blender/geometry/intern/reorder.cc b/source/blender/geometry/intern/reorder.cc
index 0c5f14ff9b2..1007657e264 100644
--- a/source/blender/geometry/intern/reorder.cc
+++ b/source/blender/geometry/intern/reorder.cc
@@ -210,10 +210,6 @@ static void reorder_instaces_exec(const bke::Instances &src_instances,
                          old_by_new_map,
                          dst_instances.attributes_for_write());
 
-  const Span<int> old_reference_handles = src_instances.reference_handles();
-  MutableSpan<int> new_reference_handles = dst_instances.reference_handles();
-  array_utils::gather(old_reference_handles, old_by_new_map, new_reference_handles);
-
   const Span<float4x4> old_transforms = src_instances.transforms();
   MutableSpan<float4x4> new_transforms = dst_instances.transforms();
   array_utils::gather(old_transforms, old_by_new_map, new_transforms);
diff --git a/source/blender/nodes/geometry/nodes/node_geo_duplicate_elements.cc b/source/blender/nodes/geometry/nodes/node_geo_duplicate_elements.cc
index f52ff22a86d..319a2553da9 100644
--- a/source/blender/nodes/geometry/nodes/node_geo_duplicate_elements.cc
+++ b/source/blender/nodes/geometry/nodes/node_geo_duplicate_elements.cc
@@ -956,13 +956,13 @@ static void duplicate_instances(GeometrySet &geometry_set,
     const int new_handle = dst_instances->add_reference(reference);
     const float4x4 transform = src_instances.transforms()[i_selection];
     dst_instances->transforms().slice(range).fill(transform);
-    dst_instances->reference_handles().slice(range).fill(new_handle);
+    dst_instances->reference_handles_for_write().slice(range).fill(new_handle);
   }
 
   bke::gather_attributes_to_groups(src_instances.attributes(),
                                    AttrDomain::Instance,
                                    propagation_info,
-                                   {"id"},
+                                   {"id", ".reference_index"},
                                    duplicates,
                                    selection,
                                    dst_instances->attributes_for_write());
diff --git a/source/blender/nodes/geometry/nodes/node_geo_instance_on_points.cc b/source/blender/nodes/geometry/nodes/node_geo_instance_on_points.cc
index a186cbf6baf..d43059578e9 100644
--- a/source/blender/nodes/geometry/nodes/node_geo_instance_on_points.cc
+++ b/source/blender/nodes/geometry/nodes/node_geo_instance_on_points.cc
@@ -85,7 +85,8 @@ static void add_instances_from_component(
   const int select_len = selection.index_range().size();
   dst_component.resize(start_len + select_len);
 
-  MutableSpan<int> dst_handles = dst_component.reference_handles().slice(start_len, select_len);
+  MutableSpan<int> dst_handles = dst_component.reference_handles_for_write().slice(start_len,
+                                                                                   select_len);
   MutableSpan<float4x4> dst_transforms = dst_component.transforms().slice(start_len, select_len);
 
   const VArraySpan positions = *src_attributes.lookup<float3>("position");
@@ -213,6 +214,7 @@ static void node_geo_exec(GeoNodeExecParams params)
                                                    propagation_info,
                                                    attributes_to_propagate);
     attributes_to_propagate.remove("position");
+    attributes_to_propagate.remove(".reference_index");
 
     for (const GeometryComponent::Type type : types) {
       if (geometry_set.has(type)) {
diff --git a/source/blender/nodes/geometry/nodes/node_geo_split_to_instances.cc b/source/blender/nodes/geometry/nodes/node_geo_split_to_instances.cc
index 0ea24934dfe..2fd9da1203f 100644
--- a/source/blender/nodes/geometry/nodes/node_geo_split_to_instances.cc
+++ b/source/blender/nodes/geometry/nodes/node_geo_split_to_instances.cc
@@ -264,8 +264,6 @@ static void split_instance_groups(const InstancesComponent &component,
       }
 
       array_utils::gather(src_instances.transforms(), mask, group_instances->transforms());
-      array_utils::gather(
-          src_instances.reference_handles(), mask, group_instances->reference_handles());
       bke::gather_attributes(src_instances.attributes(),
                              AttrDomain::Instance,
                              propagation_info,
@@ -343,7 +341,7 @@ static void node_geo_exec(GeoNodeExecParams params)
   }
 
   dst_instances->transforms().fill(float4x4::identity());
-  array_utils::fill_index_range(dst_instances->reference_handles());
+  array_utils::fill_index_range(dst_instances->reference_handles_for_write());
 
   for (auto item : geometry_by_group_id.items()) {
     std::unique_ptr<GeometrySet> &group_geometry = item.value;
diff --git a/source/blender/nodes/geometry/nodes/node_geo_string_to_curves.cc b/source/blender/nodes/geometry/nodes/node_geo_string_to_curves.cc
index 36229517354..730ce16a1d9 100644
--- a/source/blender/nodes/geometry/nodes/node_geo_string_to_curves.cc
+++ b/source/blender/nodes/geometry/nodes/node_geo_string_to_curves.cc
@@ -319,7 +319,7 @@ static void add_instances_from_handles(bke::Instances &instances,
                                        const TextLayout &layout)
 {
   instances.resize(layout.positions.size());
-  MutableSpan<int> handles = instances.reference_handles();
+  MutableSpan<int> handles = instances.reference_handles_for_write();
   MutableSpan<float4x4> transforms = instances.transforms();
 
   threading::parallel_for(IndexRange(layout.positions.size()), 256, [&](IndexRange range) {