diff --git a/sys/auto_init/auto_init.c b/sys/auto_init/auto_init.c
index 5ab321c1ab..6d1e179f45 100644
--- a/sys/auto_init/auto_init.c
+++ b/sys/auto_init/auto_init.c
@@ -392,7 +392,7 @@ void auto_init(void)
         extern void auto_init_random(void);
         auto_init_random();
     }
-    if (IS_USED(MODULE_ZTIMER)) {
+    if (IS_USED(MODULE_AUTO_INIT_ZTIMER)) {
         LOG_DEBUG("Auto init ztimer.\n");
         void ztimer_init(void);
         ztimer_init();
diff --git a/sys/ztimer/Makefile.dep b/sys/ztimer/Makefile.dep
index b9e0287fa1..fcfc495b60 100644
--- a/sys/ztimer/Makefile.dep
+++ b/sys/ztimer/Makefile.dep
@@ -5,10 +5,23 @@
 
 # "ztimer" is the default meta-module of ztimer
 ifneq (,$(filter ztimer,$(USEMODULE)))
-  USEMODULE += ztimer_auto_init
   USEMODULE += ztimer_core
   USEMODULE += ztimer_convert_frac
   USEMODULE += ztimer_convert_shift
+
+  # ztimer's auto_init code resides in it's submodule "ztimer_auto_init",
+  # but RIOT's auto_init scheme expects "auto_init_ztimer" in DEFAULT_MODULES so
+  # it can be disabled (by adding to DISABLE_MODULES).
+  #
+  # "auto_init_%" modules cannot have further dependencies, so we cannot do
+  # "if auto_init_ztimer: use ztimer_auto_init".
+  #
+  # So, if neither "auto_init" nor "auto_init_ztimer" are disabled, pull in
+  # "ztimer_auto_init".
+  DEFAULT_MODULE += auto_init_ztimer
+  ifeq (,$(filter auto_init auto_init_ztimer,$(DISABLE_MODULE)))
+    USEMODULE += ztimer_auto_init
+  endif
 endif
 
 # "ztimer_xtimer_compat" is a wrapper of the xtimer API on ztimer_used