diff --git a/src/compiler/spirv/spirv_to_nir.c b/src/compiler/spirv/spirv_to_nir.c
index bdb969a8324..5b1ae9490dc 100644
--- a/src/compiler/spirv/spirv_to_nir.c
+++ b/src/compiler/spirv/spirv_to_nir.c
@@ -5721,6 +5721,9 @@ vtn_create_builder(const uint32_t *words, size_t word_count,
    b->value_id_bound = value_id_bound;
    b->values = rzalloc_array(b, struct vtn_value, value_id_bound);
 
+   if (b->options->environment == NIR_SPIRV_VULKAN)
+      b->vars_used_indirectly = _mesa_pointer_set_create(b);
+
    return b;
  fail:
    ralloc_free(b);
@@ -5798,6 +5801,13 @@ vtn_emit_kernel_entry_point_wrapper(struct vtn_builder *b,
    return main_entry_point;
 }
 
+static bool
+can_remove(nir_variable *var, void *data)
+{
+   const struct set *vars_used_indirectly = data;
+   return !_mesa_set_search(vars_used_indirectly, var);
+}
+
 nir_shader *
 spirv_to_nir(const uint32_t *words, size_t word_count,
              struct nir_spirv_specialization *spec, unsigned num_spec,
@@ -5946,7 +5956,12 @@ spirv_to_nir(const uint32_t *words, size_t word_count,
     */
    nir_lower_variable_initializers(b->shader, nir_var_shader_out |
                                               nir_var_system_value);
-   nir_remove_dead_variables(b->shader, ~nir_var_function_temp, NULL);
+   const nir_remove_dead_variables_options dead_opts = {
+      .can_remove_var = can_remove,
+      .can_remove_var_data = b->vars_used_indirectly,
+   };
+   nir_remove_dead_variables(b->shader, ~nir_var_function_temp,
+                             b->vars_used_indirectly ? &dead_opts : NULL);
 
    /* We sometimes generate bogus derefs that, while never used, give the
     * validator a bit of heartburn.  Run dead code to get rid of them.
diff --git a/src/compiler/spirv/vtn_private.h b/src/compiler/spirv/vtn_private.h
index f230e6e8152..e3ea3eb25c0 100644
--- a/src/compiler/spirv/vtn_private.h
+++ b/src/compiler/spirv/vtn_private.h
@@ -674,6 +674,13 @@ struct vtn_builder {
     */
    struct hash_table *phi_table;
 
+   /* In Vulkan, when lowering some modes variable access, the derefs of the
+    * variables are replaced with a resource index intrinsics, leaving the
+    * variable hanging.  This set keeps track of them so they can be filtered
+    * (and not removed) in nir_remove_dead_variables.
+    */
+   struct set *vars_used_indirectly;
+
    unsigned num_specializations;
    struct nir_spirv_specialization *specializations;
 
diff --git a/src/compiler/spirv/vtn_variables.c b/src/compiler/spirv/vtn_variables.c
index 6cccb540090..1481e6b4e57 100644
--- a/src/compiler/spirv/vtn_variables.c
+++ b/src/compiler/spirv/vtn_variables.c
@@ -237,6 +237,11 @@ vtn_variable_resource_index(struct vtn_builder *b, struct vtn_variable *var,
       desc_array_index = nir_imm_int(&b->nb, 0);
    }
 
+   if (b->vars_used_indirectly) {
+      vtn_assert(var->var);
+      _mesa_set_add(b->vars_used_indirectly, var->var);
+   }
+
    nir_intrinsic_instr *instr =
       nir_intrinsic_instr_create(b->nb.shader,
                                  nir_intrinsic_vulkan_resource_index);