diff --git a/docs/02.API-REFERENCE.md b/docs/02.API-REFERENCE.md
index 8ae5e6fa3..1cfb909c0 100644
--- a/docs/02.API-REFERENCE.md
+++ b/docs/02.API-REFERENCE.md
@@ -9,7 +9,7 @@ Enum that contains the following elements:
  - JERRY_INIT_SHOW_REGEXP_OPCODES - dump regexp byte-code to log after compilation
  - JERRY_INIT_MEM_STATS - dump memory statistics
  - JERRY_INIT_MEM_STATS_SEPARATE - dump memory statistics and reset peak values after parse
- - JERRY_INIT_DEBUGGER - enable all features required by debugging
+ - JERRY_INIT_DEBUGGER - deprecated, an unused placeholder now
 
 ## jerry_error_t
 
@@ -319,7 +319,7 @@ jerry_init (jerry_init_flag_t flags)
 - `JERRY_INIT_SHOW_REGEXP_OPCODES` - print compiled regexp byte-code.
 - `JERRY_INIT_MEM_STATS` - dump memory statistics.
 - `JERRY_INIT_MEM_STATS_SEPARATE` - dump memory statistics and reset peak values after parse.
-- `JERRY_INIT_DEBUGGER` - enable all features required by debugging.
+- `JERRY_INIT_DEBUGGER` - deprecated, an unused placeholder now
 
 **Example**
 
diff --git a/docs/07.DEBUGGER.md b/docs/07.DEBUGGER.md
index 465468aae..b12f5eb06 100644
--- a/docs/07.DEBUGGER.md
+++ b/docs/07.DEBUGGER.md
@@ -65,8 +65,8 @@ All available commands of the client can be queried by the
 
 ## Integrating debugger support into applications using JerryScript
 
-The debugger can be enabled by passing the `JERRY_INIT_DEBUGGER` flag
-to the `jerry_init ()` function which then initializes the debugger
+The debugger can be enabled by calling the `jerry_debugger_init (uint16_t port)`
+function after the `jerry_init ()` function. It initializes the debugger
 and blocks until a client connects.
 
 When the debugger is enabled it is recommended to use
@@ -83,6 +83,36 @@ debugger is disabled.
 The following section describes the debugger functions
 available for the host application.
 
+### jerry_debugger_init
+
+**Summary**
+
+Debugger server initialization. Must be called after `jerry_init`.
+
+**Prototype**
+
+```c
+void
+jerry_debugger_init (uint16_t port);
+```
+
+- `port` - Server port number
+
+
+**Example**
+
+```c
+{
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
+
+  // ...
+
+  jerry_cleanup ();
+}
+```
+
+
 ### jerry_debugger_is_connected
 
 **Summary**
@@ -100,12 +130,15 @@ jerry_debugger_is_connected (void);
 
 ```c
 {
-  jerry_init (JERRY_INIT_DEBUGGER);
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
 
   if (jerry_debugger_is_connected ())
   {
     printf ("A remote debugger client is connected.");
   }
+
+  jerry_cleanup ();
 }
 ```
 
@@ -129,9 +162,12 @@ jerry_debugger_stop (void)
 
 ```c
 {
-  jerry_init (JERRY_INIT_DEBUGGER);
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
 
   jerry_debugger_stop ();
+
+  jerry_cleanup ();
 }
 ```
 
@@ -160,9 +196,12 @@ jerry_debugger_continue (void)
 
 ```c
 {
-  jerry_init (JERRY_INIT_DEBUGGER);
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
 
   jerry_debugger_continue ();
+
+  jerry_cleanup ();
 }
 ```
 
@@ -191,7 +230,8 @@ jerry_debugger_stop_at_breakpoint (bool enable_stop_at_breakpoint)
 
 ```c
 {
-  jerry_init (JERRY_INIT_DEBUGGER);
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
 
   jerry_debugger_stop_at_breakpoint (true);
 
@@ -199,6 +239,8 @@ jerry_debugger_stop_at_breakpoint (bool enable_stop_at_breakpoint)
   jerry_eval (...);
 
   jerry_debugger_stop_at_breakpoint (false);
+
+  jerry_cleanup ();
 }
 ```
 
@@ -221,7 +263,8 @@ jerry_debugger_wait_and_run_client_source (jerry_value_t *return_value)
 **Example**
 
 ```c
-  jerry_init (JERRY_INIT_DEBUGGER);
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
 
   jerry_value_t run_result;
   jerry_debugger_wait_and_run_type_t receive_status;
@@ -239,6 +282,8 @@ jerry_debugger_wait_and_run_client_source (jerry_value_t *return_value)
     jerry_release_value (run_result);
   }
   while (receive_status == JERRY_DEBUGGER_SOURCE_RECEIVED);
+
+  jerry_cleanup ();
 ```
 
 ### jerry_debugger_send_output
@@ -258,8 +303,13 @@ At the moment only the JS print size is implemented.
 **Example**
 
 ```c
+  jerry_init (JERRY_INIT_EMPTY);
+  jerry_debugger_init (5001);
+
   jerry_char_t my_output = "Hey, this should be sent too!";
   jerry_size_t my_output_size = sizeof (my_output);
 
   jerry_debugger_send_output (my_output, my_output_size, JERRY_DEBUGGER_OUTPUT_OK);
+
+  jerry_cleanup ();
 ```
diff --git a/jerry-core/api/jerry-debugger.c b/jerry-core/api/jerry-debugger.c
index aa6984495..f64e1f9c3 100644
--- a/jerry-core/api/jerry-debugger.c
+++ b/jerry-core/api/jerry-debugger.c
@@ -103,20 +103,6 @@ jerry_debugger_init (uint16_t port) /**< server port number */
 #endif /* JERRY_DEBUGGER */
 } /* jerry_debugger_init */
 
-/**
- * Debugger server shutdown. Must be called before jerry_cleanup.
- */
-void
-jerry_debugger_cleanup (void)
-{
-#ifdef JERRY_DEBUGGER
-  if (JERRY_CONTEXT (debugger_flags) & JERRY_DEBUGGER_CONNECTED)
-  {
-    jerry_debugger_close_connection ();
-  }
-#endif /* JERRY_DEBUGGER */
-} /* jerry_debugger_cleanup */
-
 /**
  * Sets whether the engine should wait and run a source.
  *
diff --git a/jerry-core/api/jerry.c b/jerry-core/api/jerry.c
index 5a35032af..4499ae0a7 100644
--- a/jerry-core/api/jerry.c
+++ b/jerry-core/api/jerry.c
@@ -167,6 +167,13 @@ jerry_cleanup (void)
 {
   jerry_assert_api_available ();
 
+#ifdef JERRY_DEBUGGER
+  if (JERRY_CONTEXT (debugger_flags) & JERRY_DEBUGGER_CONNECTED)
+  {
+    jerry_debugger_close_connection ();
+  }
+#endif /* JERRY_DEBUGGER */
+
   for (jerry_context_data_header_t *this_p = JERRY_CONTEXT (context_data_p), *next_p = NULL;
        this_p != NULL;
        this_p = next_p)
diff --git a/jerry-core/include/jerryscript-debugger.h b/jerry-core/include/jerryscript-debugger.h
index 730504bd2..c4f01e0dc 100644
--- a/jerry-core/include/jerryscript-debugger.h
+++ b/jerry-core/include/jerryscript-debugger.h
@@ -40,6 +40,7 @@ typedef enum
 /**
  * Engine debugger functions.
  */
+void jerry_debugger_init (uint16_t port);
 bool jerry_debugger_is_connected (void);
 void jerry_debugger_stop (void);
 void jerry_debugger_continue (void);
@@ -47,9 +48,6 @@ void jerry_debugger_stop_at_breakpoint (bool enable_stop_at_breakpoint);
 jerry_debugger_wait_and_run_type_t jerry_debugger_wait_and_run_client_source (jerry_value_t *return_value);
 void jerry_debugger_send_output (jerry_char_t buffer[], jerry_size_t str_size, uint8_t type);
 
-void jerry_debugger_init (uint16_t port);
-void jerry_debugger_cleanup (void);
-
 /**
  * @}
  */
diff --git a/jerry-main/main-unix.c b/jerry-main/main-unix.c
index 42e98db81..c7afe1b1a 100644
--- a/jerry-main/main-unix.c
+++ b/jerry-main/main-unix.c
@@ -830,10 +830,6 @@ main (int argc,
 
   jerry_release_value (ret_value);
 
-  if (start_debug_server)
-  {
-    jerry_debugger_cleanup ();
-  }
   jerry_cleanup ();
 #ifdef JERRY_ENABLE_EXTERNAL_CONTEXT
   free (instance_p);
diff --git a/targets/nuttx-stm32f4/Kconfig b/targets/nuttx-stm32f4/Kconfig
index 6f8ff369a..0682aaff6 100644
--- a/targets/nuttx-stm32f4/Kconfig
+++ b/targets/nuttx-stm32f4/Kconfig
@@ -46,11 +46,4 @@ config JERRYSCRIPT_SHOW_OPCODES
 config JERRYSCRIPT_DEBUGGER
 	bool "Jerryscript debugger"
 	default n
-
-if JERRYSCRIPT_DEBUGGER
-config JERRYSCRIPT_DEBUGGER_PORT
-	int "Jerryscript debugger port"
-	default 5001
-endif
-
 endif
diff --git a/targets/nuttx-stm32f4/Makefile b/targets/nuttx-stm32f4/Makefile
index e35c6095b..46077c763 100644
--- a/targets/nuttx-stm32f4/Makefile
+++ b/targets/nuttx-stm32f4/Makefile
@@ -19,7 +19,6 @@
 CONFIG_JERRYSCRIPT_PRIORITY ?= SCHED_PRIORITY_DEFAULT
 CONFIG_JERRYSCRIPT_STACKSIZE ?= 16384
 CONFIG_JERRYSCRIPT_HEAPSIZE ?= 107520
-CONFIG_JERRY_DEBUGGER_PORT ?= 5001
 
 APPNAME = jerry
 # path to the project dir, "jerry-nuttx" by default
@@ -45,7 +44,7 @@ ifeq ($(CONFIG_JERRYSCRIPT_SHOW_OPCODES),y)
 endif
 
 ifeq ($(CONFIG_JERRYSCRIPT_DEBUGGER),y)
-	CFLAGS += -DJERRY_DEBUGGER '-DJERRY_DEBUGGER_PORT=$(CONFIG_JERRY_DEBUGGER_PORT)'
+	CFLAGS += -DJERRY_DEBUGGER
 endif
 
 # Jerryscript
diff --git a/targets/nuttx-stm32f4/jerry_main.c b/targets/nuttx-stm32f4/jerry_main.c
index de36b4ec7..97f4d52e6 100644
--- a/targets/nuttx-stm32f4/jerry_main.c
+++ b/targets/nuttx-stm32f4/jerry_main.c
@@ -53,6 +53,7 @@ print_help (char *name)
           "  --mem-stats-separate\n"
           "  --show-opcodes\n"
           "  --start-debug-server\n"
+          "  --debug-server-port [port]\n"
           "\n",
           name);
 } /* print_help */
@@ -357,6 +358,8 @@ int jerry_main (int argc, char *argv[])
   const char *file_names[JERRY_MAX_COMMAND_LINE_ARGS];
   int i;
   int files_counter = 0;
+  bool start_debug_server = false;
+  uint16_t debug_port = 5001;
 
   jerry_init_flag_t flags = JERRY_INIT_EMPTY;
 
@@ -396,7 +399,19 @@ int jerry_main (int argc, char *argv[])
     }
     else if (!strcmp ("--start-debug-server", argv[i]))
     {
-      flags |= JERRY_INIT_DEBUGGER;
+      start_debug_server = true;
+    }
+    else if (!strcmp ("--debug-server-port", argv[i]))
+    {
+      if (++i < argc)
+      {
+        debug_port = str_to_uint (argv[i]);
+      }
+      else
+      {
+        jerry_port_log (JERRY_LOG_LEVEL_ERROR, "Error: wrong format or invalid argument\n");
+        return JERRY_STANDALONE_EXIT_CODE_FAIL;
+      }
     }
     else
     {
@@ -406,6 +421,11 @@ int jerry_main (int argc, char *argv[])
 
   jerry_init (flags);
 
+  if (start_debug_server)
+  {
+    jerry_debugger_init (debug_port);
+  }
+
   register_js_function ("assert", jerryx_handler_assert);
   register_js_function ("gc", jerryx_handler_gc);
   register_js_function ("print", jerryx_handler_print);
diff --git a/targets/tizenrt-artik053/apps/jerryscript/Kconfig b/targets/tizenrt-artik053/apps/jerryscript/Kconfig
index 6f8ff369a..0682aaff6 100644
--- a/targets/tizenrt-artik053/apps/jerryscript/Kconfig
+++ b/targets/tizenrt-artik053/apps/jerryscript/Kconfig
@@ -46,11 +46,4 @@ config JERRYSCRIPT_SHOW_OPCODES
 config JERRYSCRIPT_DEBUGGER
 	bool "Jerryscript debugger"
 	default n
-
-if JERRYSCRIPT_DEBUGGER
-config JERRYSCRIPT_DEBUGGER_PORT
-	int "Jerryscript debugger port"
-	default 5001
-endif
-
 endif
diff --git a/targets/tizenrt-artik053/apps/jerryscript/Makefile b/targets/tizenrt-artik053/apps/jerryscript/Makefile
index 0d5e2d553..0b166a895 100644
--- a/targets/tizenrt-artik053/apps/jerryscript/Makefile
+++ b/targets/tizenrt-artik053/apps/jerryscript/Makefile
@@ -72,7 +72,6 @@ include $(APPDIR)/Make.defs
 CONFIG_JERRYSCRIPT_PRIORITY ?= SCHED_PRIORITY_DEFAULT
 CONFIG_JERRYSCRIPT_STACKSIZE ?= 32768
 CONFIG_JERRYSCRIPT_HEAPSIZE ?= 64000
-CONFIG_JERRY_DEBUGGER_PORT ?= 5001
 
 APPNAME = jerry
 # path to the project dir, "tizenrt-artik053" by default
@@ -92,7 +91,7 @@ ifeq ($(CONFIG_JERRYSCRIPT_SHOW_OPCODES),y)
 endif
 
 ifeq ($(CONFIG_JERRYSCRIPT_DEBUGGER),y)
-	CFLAGS += -DJERRY_DEBUGGER '-DJERRY_DEBUGGER_PORT=$(CONFIG_JERRY_DEBUGGER_PORT)'
+	CFLAGS += -DJERRY_DEBUGGER
 endif
 
 
diff --git a/targets/tizenrt-artik053/apps/jerryscript/jerry_main.c b/targets/tizenrt-artik053/apps/jerryscript/jerry_main.c
index 9ea520230..21c33bb7c 100644
--- a/targets/tizenrt-artik053/apps/jerryscript/jerry_main.c
+++ b/targets/tizenrt-artik053/apps/jerryscript/jerry_main.c
@@ -333,6 +333,8 @@ jerry_cmd_main (int argc, char *argv[])
   const char *file_names[JERRY_MAX_COMMAND_LINE_ARGS];
   int i;
   int files_counter = 0;
+  bool start_debug_server = false;
+  uint16_t debug_port = 5001;
 
   jerry_init_flag_t flags = JERRY_INIT_EMPTY;
 
@@ -372,7 +374,19 @@ jerry_cmd_main (int argc, char *argv[])
     }
     else if (!strcmp ("--start-debug-server", argv[i]))
     {
-      flags |= JERRY_INIT_DEBUGGER;
+      start_debug_server = true;
+    }
+    else if (!strcmp ("--debug-server-port", argv[i]))
+    {
+      if (++i < argc)
+      {
+        debug_port = str_to_uint (argv[i]);
+      }
+      else
+      {
+        jerry_port_log (JERRY_LOG_LEVEL_ERROR, "Error: wrong format or invalid argument\n");
+        return JERRY_STANDALONE_EXIT_CODE_FAIL;
+      }
     }
     else
     {
@@ -382,6 +396,11 @@ jerry_cmd_main (int argc, char *argv[])
 
   jerry_init (flags);
 
+  if (start_debug_server)
+  {
+    jerry_debugger_init (debug_port);
+  }
+
   register_js_function ("assert", jerryx_handler_assert);
   register_js_function ("gc", jerryx_handler_gc);
   register_js_function ("print", jerryx_handler_print);