diff --git a/src/com/android/settings/inputmethod/InputMethodAndSubtypeEnabler.java b/src/com/android/settings/inputmethod/InputMethodAndSubtypeEnabler.java
index b6663184791..03e97ff5095 100644
--- a/src/com/android/settings/inputmethod/InputMethodAndSubtypeEnabler.java
+++ b/src/com/android/settings/inputmethod/InputMethodAndSubtypeEnabler.java
@@ -121,8 +121,6 @@ public class InputMethodAndSubtypeEnabler extends SettingsPreferenceFragment
     @Override
     public void onPause() {
         super.onPause();
-        // Clear all subtypes of all IMEs to make sure
-        updateImplicitlyEnabledSubtypes(null /* targetImiId */, false /* check */);
         InputMethodAndSubtypeUtil.saveInputMethodSubtypeList(this, getContentResolver(),
                 mInputMethodInfoList, mHaveHardKeyboard);
     }
diff --git a/src/com/android/settings/inputmethod/InputMethodAndSubtypeUtil.java b/src/com/android/settings/inputmethod/InputMethodAndSubtypeUtil.java
index dfa16340e1e..b79f44d7f2e 100644
--- a/src/com/android/settings/inputmethod/InputMethodAndSubtypeUtil.java
+++ b/src/com/android/settings/inputmethod/InputMethodAndSubtypeUtil.java
@@ -209,7 +209,12 @@ class InputMethodAndSubtypeUtil {
                         needsToResetSelectedSubtype = true;
                         subtypePrefFound = true;
                     }
-                    if (subtypePref.isChecked()) {
+                    // Checking <code>subtypePref.isEnabled()</code> is insufficient to determine
+                    // whether the user manually enabled this subtype or not.  Implicitly-enabled
+                    // subtypes are also checked just as an indicator to users.  We also need to
+                    // check <code>subtypePref.isEnabled()</code> so that only manually enabled
+                    // subtypes can be saved here.
+                    if (subtypePref.isEnabled() && subtypePref.isChecked()) {
                         subtypesSet.add(subtypeHashCodeStr);
                         if (isCurrentInputMethod) {
                             if (selectedInputMethodSubtype == subtype.hashCode()) {