diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3a10cf465..6bcf5acf2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -429,7 +429,7 @@ foreach(_SUB ${SDL_X11_OPTIONS})
 endforeach()
 set_option(SDL_WAYLAND             "Use Wayland video driver" ${UNIX_SYS})
 dep_option(SDL_WAYLAND_SHARED      "Dynamically load Wayland support" ON "SDL_WAYLAND" OFF)
-dep_option(SDL_WAYLAND_LIBDECOR    "Use client-side window decorations on Wayland" ON "SDL_WAYLAND" ON)
+dep_option(SDL_WAYLAND_LIBDECOR    "Use client-side window decorations on Wayland" ON "SDL_WAYLAND" OFF)
 dep_option(SDL_WAYLAND_LIBDECOR_SHARED     "Dynamically load libdecor support" ON "SDL_WAYLAND_LIBDECOR" OFF)
 dep_option(SDL_WAYLAND_QT_TOUCH    "QtWayland server support for Wayland video driver" ON "SDL_WAYLAND" OFF)
 set_option(SDL_RPI                 "Use Raspberry Pi video driver" ${UNIX_SYS})
diff --git a/configure b/configure
index 5632de25a..3545f72e6 100755
--- a/configure
+++ b/configure
@@ -17954,7 +17954,12 @@ SOURCES="$SOURCES $srcdir/src/locale/*.c"
 if test "${enable_atomic+set}" = set; then :
   enableval=$enable_atomic;
 else
-  enable_atomic=yes
+  case "$host" in
+        *-*-emscripten*)
+                enable_atomic=no;;
+        *)
+                enable_atomic=yes;;
+  esac
 fi
 
 if test x$enable_atomic != xyes; then
diff --git a/configure.ac b/configure.ac
index b5fe9a433..48c61c081 100644
--- a/configure.ac
+++ b/configure.ac
@@ -415,9 +415,18 @@ SOURCES="$SOURCES $srcdir/src/locale/*.c"
 
 dnl Enable/disable various subsystems of the SDL library
 
+case "$host" in
+    *-*-emscripten*)
+        default_atomic=no
+        ;;
+    *)
+        default_atomic=yes
+        ;;
+esac
+
 AC_ARG_ENABLE(atomic,
 [AS_HELP_STRING([--enable-atomic], [Enable the atomic operations subsystem [default=yes]])],
-              , enable_atomic=yes)
+              , enable_atomic=$default_atomic)
 if test x$enable_atomic != xyes; then
     AC_DEFINE(SDL_ATOMIC_DISABLED, 1, [ ])
 else