diff --git a/bootloaders/riotboot_dfu/Makefile b/bootloaders/riotboot_dfu/Makefile
index 4a943449c9..615e7dd09c 100644
--- a/bootloaders/riotboot_dfu/Makefile
+++ b/bootloaders/riotboot_dfu/Makefile
@@ -6,7 +6,7 @@ USEMODULE += riotboot_usb_dfu
 
 # Use xtimer for scheduled reboot
 USEMODULE += ztimer
-USEMODULE += ztimer_auto_init
+USEMODULE += ztimer_init
 
 # USB device vendor and product ID
 # pid.codes test VID/PID, not globally unique
diff --git a/sys/ztimer/Kconfig b/sys/ztimer/Kconfig
index daad9f11b1..2537cb7367 100644
--- a/sys/ztimer/Kconfig
+++ b/sys/ztimer/Kconfig
@@ -171,13 +171,10 @@ config MODULE_ZTIMER
 
 if MODULE_ZTIMER
 
-# TODO: only use MODULE_ZTIMER_AUTO_INIT, for now we try to get the same modules
-# as the Makefile dependency resolution. See sys/ztimer/Makefile.dep for more
-# info on why two modules are used.
 config MODULE_AUTO_INIT_ZTIMER
     bool "Auto initialize ztimer"
     depends on MODULE_AUTO_INIT
-    select MODULE_ZTIMER_AUTO_INIT
+    select MODULE_ZTIMER_INIT
     default y
 
 config MODULE_ZTIMER_NOW64
@@ -194,7 +191,7 @@ config MODULE_ZTIMER_MOCK
         manually fired to simulate different scenarios and test the ztimer
         implementation using this as a backing timer.
 
-config MODULE_ZTIMER_AUTO_INIT
+config MODULE_ZTIMER_INIT
     bool
 
 config MODULE_ZTIMER_CORE
diff --git a/sys/ztimer/Makefile.dep b/sys/ztimer/Makefile.dep
index 131efa2160..f92d76d74d 100644
--- a/sys/ztimer/Makefile.dep
+++ b/sys/ztimer/Makefile.dep
@@ -7,20 +7,11 @@ ifneq (,$(filter ztimer,$(USEMODULE)))
   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
+  ifneq (,$(filter auto_init_ztimer,$(USEMODULE)))
+    USEMODULE += ztimer_init
   endif
+  DEFAULT_MODULE += auto_init_ztimer
+  DEFAULT_MODULE += ztimer_init
 endif
 
 # unless ztimer_xtimer_compat is used, make xtimer use ztimer_usec as backend.
diff --git a/sys/ztimer/auto_init.c b/sys/ztimer/init.c
similarity index 98%
rename from sys/ztimer/auto_init.c
rename to sys/ztimer/init.c
index b24fdeb1fe..6436103f91 100644
--- a/sys/ztimer/auto_init.c
+++ b/sys/ztimer/init.c
@@ -37,7 +37,6 @@
  */
 
 #include "kernel_defines.h"
-#if IS_USED(MODULE_AUTO_INIT_ZTIMER) || RIOTBOOT
 
 #include "board.h"
 #include "ztimer.h"
@@ -302,4 +301,3 @@ void ztimer_init(void)
 #  endif
 #endif
 }
-#endif /* IS_USED(MODULE_AUTO_INIT_ZTIMER) || RIOTBOOT*/