diff --git a/boards/native/Makefile.include b/boards/native/Makefile.include
index dece98a972..564e375eb3 100644
--- a/boards/native/Makefile.include
+++ b/boards/native/Makefile.include
@@ -73,7 +73,15 @@ ifneq (,$(filter netdev_default gnrc_netdev_default,$(USEMODULE)))
   PORT ?= tap0
 endif
 
-TERMFLAGS := $(PORT) $(TERMFLAGS)
+# Configure default eeprom file
+EEPROM_FILE ?= $(BINDIR)/native.eeprom
+
+# set the eeprom file flags only when the periph_eeprom feature is used.
+# NOTE: This can be turned into normal conditional syntax once #9913 is fixed
+EEPROM_FILE_FLAGS = $(if $(filter periph_eeprom,$(FEATURES_USED)),--eeprom $(EEPROM_FILE),)
+TERMFLAGS += $(EEPROM_FILE_FLAGS)
+
+TERMFLAGS += $(PORT)
 
 ASFLAGS =
 ifeq ($(shell basename $(DEBUGGER)),lldb)
diff --git a/cpu/native/include/eeprom_native.h b/cpu/native/include/eeprom_native.h
index 788405cfa2..eb1238029a 100644
--- a/cpu/native/include/eeprom_native.h
+++ b/cpu/native/include/eeprom_native.h
@@ -27,6 +27,10 @@
 extern "C" {
 #endif
 
+#ifndef EEPROM_FILEPATH_MAX_LEN
+#define EEPROM_FILEPATH_MAX_LEN     (128U) /**< Maximum path len to store the EEPROM filepath */
+#endif
+
 /**
  * @brief   Read the configured file containing the EEPROM content
  *
diff --git a/cpu/native/include/periph_cpu.h b/cpu/native/include/periph_cpu.h
index cdf3b529de..8d34804fe0 100644
--- a/cpu/native/include/periph_cpu.h
+++ b/cpu/native/include/periph_cpu.h
@@ -99,9 +99,6 @@ typedef enum {
 #ifndef EEPROM_SIZE
 #define EEPROM_SIZE             (1024U)  /* 1kB */
 #endif
-#ifndef EEPROM_FILE
-#define EEPROM_FILE             "/tmp/riot_native.eeprom"
-#endif
 /** @} */
 
 #ifdef __cplusplus
diff --git a/cpu/native/startup.c b/cpu/native/startup.c
index 9c149f203c..a9fb963dd3 100644
--- a/cpu/native/startup.c
+++ b/cpu/native/startup.c
@@ -47,10 +47,6 @@
 #include "periph/init.h"
 #include "periph/pm.h"
 
-#ifdef MODULE_PERIPH_EEPROM
-#include "eeprom_native.h"
-#endif
-
 #define ENABLE_DEBUG (0)
 #include "debug.h"
 
@@ -90,6 +86,10 @@ netdev_tap_params_t netdev_tap_params[NETDEV_TAP_MAX];
 
 socket_zep_params_t socket_zep_params[SOCKET_ZEP_MAX];
 #endif
+#ifdef MODULE_PERIPH_EEPROM
+#include "eeprom_native.h"
+extern char eeprom_file[EEPROM_FILEPATH_MAX_LEN];
+#endif
 
 static const char short_opts[] = ":hi:s:deEoc:"
 #ifdef MODULE_MTD_NATIVE
@@ -126,6 +126,9 @@ static const struct option long_opts[] = {
 #endif
 #ifdef MODULE_PERIPH_SPIDEV_LINUX
     { "spi", required_argument, NULL, 'p' },
+#endif
+#ifdef MODULE_PERIPH_EEPROM
+    { "eeprom", required_argument, NULL, 'M' },
 #endif
     { NULL, 0, NULL, '\0' },
 };
@@ -318,6 +321,12 @@ void usage_exit(int status)
 "                 SPI_DEV(0) and SPI_HWCS(1).\n"
 "        Supports up to %d buses with %d CS lines each.\n", SPI_NUMOF, SPI_MAXCS
     );
+#endif
+#ifdef MODULE_PERIPH_EEPROM
+    real_printf(
+"    -M <eeprom> , --eeprom=<eeprom>\n"
+"        Specify the file path where the EEPROM content is stored\n"
+"        Example: --eeprom=/tmp/riot_native.eeprom\n");
 #endif
     real_exit(status);
 }
@@ -504,6 +513,12 @@ __attribute__((constructor)) static void startup(int argc, char **argv, char **e
                     }
                 }
                 break;
+#endif
+#ifdef MODULE_PERIPH_EEPROM
+            case 'M': {
+                strncpy(eeprom_file, optarg, EEPROM_FILEPATH_MAX_LEN);
+                break;
+            }
 #endif
             default:
                 usage_exit(EXIT_FAILURE);