diff --git a/core/io/logger.cpp b/core/io/logger.cpp
index bd0285a7a9f..8a07459a1df 100644
--- a/core/io/logger.cpp
+++ b/core/io/logger.cpp
@@ -43,6 +43,12 @@ bool Logger::should_log(bool p_err) {
 	return (!p_err || _print_error_enabled) && (p_err || _print_line_enabled);
 }
 
+bool Logger::_flush_stdout_on_print = true;
+
+void Logger::set_flush_stdout_on_print(bool value) {
+	_flush_stdout_on_print = value;
+}
+
 void Logger::log_error(const char *p_function, const char *p_file, int p_line, const char *p_code, const char *p_rationale, ErrorType p_type) {
 	if (!should_log(true)) {
 		return;
@@ -207,7 +213,7 @@ void RotatedFileLogger::logv(const char *p_format, va_list p_list, bool p_err) {
 			Memory::free_static(buf);
 		}
 
-		if (p_err || !ProjectSettings::get_singleton() || GLOBAL_GET("application/run/flush_stdout_on_print")) {
+		if (p_err || _flush_stdout_on_print) {
 			// Don't always flush when printing stdout to avoid performance
 			// issues when `print()` is spammed in release builds.
 			file->flush();
@@ -228,7 +234,7 @@ void StdLogger::logv(const char *p_format, va_list p_list, bool p_err) {
 		vfprintf(stderr, p_format, p_list);
 	} else {
 		vprintf(p_format, p_list);
-		if (!ProjectSettings::get_singleton() || GLOBAL_GET("application/run/flush_stdout_on_print")) {
+		if (_flush_stdout_on_print) {
 			// Don't always flush when printing stdout to avoid performance
 			// issues when `print()` is spammed in release builds.
 			fflush(stdout);
diff --git a/core/io/logger.h b/core/io/logger.h
index b8e615b436d..a12945911c9 100644
--- a/core/io/logger.h
+++ b/core/io/logger.h
@@ -41,6 +41,8 @@ class Logger {
 protected:
 	bool should_log(bool p_err);
 
+	static bool _flush_stdout_on_print;
+
 public:
 	enum ErrorType {
 		ERR_ERROR,
@@ -49,6 +51,8 @@ public:
 		ERR_SHADER
 	};
 
+	static void set_flush_stdout_on_print(bool value);
+
 	virtual void logv(const char *p_format, va_list p_list, bool p_err) _PRINTF_FORMAT_ATTRIBUTE_2_0 = 0;
 	virtual void log_error(const char *p_function, const char *p_file, int p_line, const char *p_code, const char *p_rationale, ErrorType p_type = ERR_ERROR);
 
diff --git a/doc/classes/ProjectSettings.xml b/doc/classes/ProjectSettings.xml
index b68ca2ac67e..a1e5e60b4aa 100644
--- a/doc/classes/ProjectSettings.xml
+++ b/doc/classes/ProjectSettings.xml
@@ -273,9 +273,11 @@
 			If [code]true[/code], flushes the standard output stream every time a line is printed. This affects both terminal logging and file logging.
 			When running a project, this setting must be enabled if you want logs to be collected by service managers such as systemd/journalctl. This setting is disabled by default on release builds, since flushing on every printed line will negatively affect performance if lots of lines are printed in a rapid succession. Also, if this setting is enabled, logged files will still be written successfully if the application crashes or is otherwise killed by the user (without being closed "normally").
 			[b]Note:[/b] Regardless of this setting, the standard error stream ([code]stderr[/code]) is always flushed when a line is printed to it.
+			Changes to this setting will only be applied upon restarting the application.
 		</member>
 		<member name="application/run/flush_stdout_on_print.debug" type="bool" setter="" getter="" default="true">
 			Debug build override for [member application/run/flush_stdout_on_print], as performance is less important during debugging.
+			Changes to this setting will only be applied upon restarting the application.
 		</member>
 		<member name="application/run/frame_delay_msec" type="int" setter="" getter="" default="0">
 			Forces a delay between frames in the main loop (in milliseconds). This may be useful if you plan to disable vertical synchronization.
diff --git a/main/main.cpp b/main/main.cpp
index e9b06f6b077..884caab1e94 100644
--- a/main/main.cpp
+++ b/main/main.cpp
@@ -538,8 +538,8 @@ Error Main::setup(const char *execpath, int argc, char *argv[], bool p_second_ph
 
 	// Only flush stdout in debug builds by default, as spamming `print()` will
 	// decrease performance if this is enabled.
-	GLOBAL_DEF("application/run/flush_stdout_on_print", false);
-	GLOBAL_DEF("application/run/flush_stdout_on_print.debug", true);
+	GLOBAL_DEF_RST("application/run/flush_stdout_on_print", false);
+	GLOBAL_DEF_RST("application/run/flush_stdout_on_print.debug", true);
 
 	GLOBAL_DEF("debug/settings/crash_handler/message",
 			String("Please include this when reporting the bug on https://github.com/godotengine/godot/issues"));
@@ -1174,6 +1174,8 @@ Error Main::setup(const char *execpath, int argc, char *argv[], bool p_second_ph
 		_print_line_enabled = false;
 	}
 
+	Logger::set_flush_stdout_on_print(ProjectSettings::get_singleton()->get("application/run/flush_stdout_on_print"));
+
 	OS::get_singleton()->set_cmdline(execpath, main_args);
 
 	GLOBAL_DEF("rendering/driver/driver_name", "Vulkan");