diff --git a/source/blender/blenloader/intern/versioning_400.cc b/source/blender/blenloader/intern/versioning_400.cc
index a6e6ce29af6..9ae8c317630 100644
--- a/source/blender/blenloader/intern/versioning_400.cc
+++ b/source/blender/blenloader/intern/versioning_400.cc
@@ -455,15 +455,6 @@ static void version_movieclips_legacy_camera_object(Main *bmain)
   }
 }
 
-static void version_geometry_nodes_add_realize_instance_nodes(bNodeTree *ntree)
-{
-  LISTBASE_FOREACH_MUTABLE (bNode *, node, &ntree->nodes) {
-    if (STREQ(node->idname, "GeometryNodeMeshBoolean")) {
-      add_realize_instances_before_socket(ntree, node, nodeFindSocket(node, SOCK_IN, "Mesh 2"));
-    }
-  }
-}
-
 /* Version VertexWeightEdit modifier to make existing weights exclusive of the threshold. */
 static void version_vertex_weight_edit_preserve_threshold_exclusivity(Main *bmain)
 {
@@ -1300,14 +1291,6 @@ void blo_do_versions_400(FileData *fd, Library * /*lib*/, Main *bmain)
     }
   }
 
-  if (!MAIN_VERSION_FILE_ATLEAST(bmain, 400, 3)) {
-    LISTBASE_FOREACH (bNodeTree *, ntree, &bmain->nodetrees) {
-      if (ntree->type == NTREE_GEOMETRY) {
-        version_geometry_nodes_add_realize_instance_nodes(ntree);
-      }
-    }
-  }
-
   /* 400 4 did not require any do_version here. */
 
   if (!MAIN_VERSION_FILE_ATLEAST(bmain, 400, 5)) {
diff --git a/source/blender/nodes/geometry/nodes/node_geo_boolean.cc b/source/blender/nodes/geometry/nodes/node_geo_boolean.cc
index 441cd30466c..efa92f5a94f 100644
--- a/source/blender/nodes/geometry/nodes/node_geo_boolean.cc
+++ b/source/blender/nodes/geometry/nodes/node_geo_boolean.cc
@@ -3,6 +3,7 @@
  * SPDX-License-Identifier: GPL-2.0-or-later */
 
 #include "BKE_geometry_set_instances.hh"
+#include "BKE_instances.hh"
 #include "BKE_mesh_boolean_convert.hh"
 
 #include "DNA_mesh_types.h"
@@ -65,6 +66,16 @@ static void node_init(bNodeTree * /*tree*/, bNode *node)
   node->custom1 = GEO_NODE_BOOLEAN_DIFFERENCE;
 }
 
+static Array<short> calc_mesh_material_map(const Mesh &mesh, VectorSet<Material *> &all_materials)
+{
+  Array<short> map(mesh.totcol);
+  for (const int i : IndexRange(mesh.totcol)) {
+    Material *material = mesh.mat[i];
+    map[i] = material ? all_materials.index_of_or_add(material) : -1;
+  }
+  return map;
+}
+
 static void node_geo_exec(GeoNodeExecParams params)
 {
 #ifdef WITH_GMP
@@ -73,6 +84,7 @@ static void node_geo_exec(GeoNodeExecParams params)
   const bool hole_tolerant = params.get_input<bool>("Hole Tolerant");
 
   Vector<const Mesh *> meshes;
+  Vector<float4x4> transforms;
   VectorSet<Material *> materials;
   Vector<Array<short>> material_remaps;
 
@@ -84,6 +96,7 @@ static void node_geo_exec(GeoNodeExecParams params)
      * to be a single mesh. */
     if (const Mesh *mesh_in_a = set_a.get_mesh()) {
       meshes.append(mesh_in_a);
+      transforms.append(float4x4::identity());
       if (mesh_in_a->totcol == 0) {
         /* Necessary for faces using the default material when there are no material slots. */
         materials.add(nullptr);
@@ -100,12 +113,39 @@ static void node_geo_exec(GeoNodeExecParams params)
   for (const GeometrySet &geometry : geometry_sets) {
     if (const Mesh *mesh = geometry.get_mesh()) {
       meshes.append(mesh);
-      Array<short> map(mesh->totcol);
-      for (const int i : IndexRange(mesh->totcol)) {
-        Material *material = mesh->mat[i];
-        map[i] = material ? materials.index_of_or_add(material) : -1;
+      transforms.append(float4x4::identity());
+      material_remaps.append(calc_mesh_material_map(*mesh, materials));
+    }
+    if (const bke::Instances *instances = geometry.get_instances()) {
+      const Span<bke::InstanceReference> references = instances->references();
+      const Span<int> handles = instances->reference_handles();
+      const Span<float4x4> instance_transforms = instances->transforms();
+      for (const int i : handles.index_range()) {
+        const bke::InstanceReference &reference = references[handles[i]];
+        switch (reference.type()) {
+          case bke::InstanceReference::Type::Object: {
+            const GeometrySet object_geometry = bke::object_get_evaluated_geometry_set(
+                reference.object());
+            if (const Mesh *mesh = object_geometry.get_mesh()) {
+              meshes.append(mesh);
+              transforms.append(instance_transforms[i]);
+              material_remaps.append(calc_mesh_material_map(*mesh, materials));
+            }
+            break;
+          }
+          case bke::InstanceReference::Type::GeometrySet: {
+            if (const Mesh *mesh = reference.geometry_set().get_mesh()) {
+              meshes.append(mesh);
+              transforms.append(instance_transforms[i]);
+              material_remaps.append(calc_mesh_material_map(*mesh, materials));
+            }
+            break;
+          }
+          case bke::InstanceReference::Type::None:
+          case bke::InstanceReference::Type::Collection:
+            break;
+        }
       }
-      material_remaps.append(std::move(map));
     }
   }
 
@@ -116,7 +156,7 @@ static void node_geo_exec(GeoNodeExecParams params)
   Vector<int> intersecting_edges;
   Mesh *result = blender::meshintersect::direct_mesh_boolean(
       meshes,
-      {},
+      transforms,
       float4x4::identity(),
       material_remaps,
       use_self,