diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 226e7f9a2..b9a2bf37f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,7 @@ This release fixes the following problems identified in fish 4.3.0:
 - Glitch with soft-wrapped autosuggestions and :doc:`cmds/fish_right_prompt` (:issue:`12255`).
 - Spurious echo in tmux when typing a command really fast (:issue:`12261`).
 - ``tomorrow`` theme always using the light variant (:issue:`12266`).
+- ``fish_config theme choose`` sometimes not shadowing themes set by e.g. webconfig (:issue:`12278`).
 - The sample prompts and themes are correctly installed (:issue:`12241`).
 - Last line of command output could be hidden when missing newline (:issue:`12246`).
 
diff --git a/share/functions/fish_config.fish b/share/functions/fish_config.fish
index ccfd6dce4..934ef89c4 100644
--- a/share/functions/fish_config.fish
+++ b/share/functions/fish_config.fish
@@ -321,10 +321,11 @@ function __fish_config_theme_choose
             else
                 set desired_color_theme $fish_terminal_color_theme
                 if not set -q desired_color_theme[1]
-                    echo >&2 "fish_config theme choose: internal error: \$fish_terminal_color_theme not yet initialized"
-                    return 1
-                end
-                if not contains -- "[$desired_color_theme]" $theme_data
+                    if test $scope = -U
+                        echo >&2 "fish_config theme save: error: \$fish_terminal_color_theme not yet initialized"
+                        return 1
+                    end
+                else if not contains -- "[$desired_color_theme]" $theme_data
                     __fish_config_theme_choose_bad_color_theme $theme_name "$desired_color_theme" \$fish_terminal_color_theme = $desired_color_theme
                     echo >&2 "fish_config theme choose: hint: if your terminal does not report colors, pass --color-theme=light or --color-theme=dark when using color-theme-aware themes"
                     return 1
@@ -342,7 +343,7 @@ function __fish_config_theme_choose
         set -l color_theme
         string match -re -- (__fish_theme_variable_filter)'|^\[.*\]$' $theme_data |
             while read -lat toks
-                if $theme_is_color_theme_aware
+                if $theme_is_color_theme_aware && set -q desired_color_theme[1]
                     for ct in $color_themes
                         if test "$toks" = [$ct]
                             set color_theme $ct
@@ -362,7 +363,11 @@ function __fish_config_theme_choose
                     set -eg $varname
                 end
                 if $override || not set -q $varname || string match -rq -- '--theme=.*' $$varname
-                    set $scope $toks (test $scope != -U && echo --theme=$theme_name)
+                    set $scope $toks[1] (
+                        if not $theme_is_color_theme_aware || set -q desired_color_theme[1]
+                            string join \n -- $toks[2..]
+                        end
+                    ) (test $scope != -U && echo --theme=$theme_name)
                 end
             end
         if $override
@@ -376,12 +381,15 @@ function __fish_config_theme_choose
             end
         end
     end
-    if test -n "$fish_terminal_color_theme" || not $need_hook
-        if set -q _flag_no_override[1]
-            __fish_apply_theme
-        else
-            __fish_override=true __fish_apply_theme
+    if not $need_hook || test -n "$fish_terminal_color_theme" ||
+            # comment to work around fish_indent bug
+            {
+                $theme_is_color_theme_aware && test -z "$fish_terminal_color_theme"
+            }
+        if not set -q _flag_no_override[1]
+            set -fx __fish_override true
         end
+        __fish_apply_theme
     end
 end
 
diff --git a/tests/checks/fish_config.fish b/tests/checks/fish_config.fish
index c42cc8136..a480705da 100644
--- a/tests/checks/fish_config.fish
+++ b/tests/checks/fish_config.fish
@@ -1,6 +1,8 @@
 # RUN: %fish %s
 # REQUIRES: command -v diff
 
+set -g fish (status fish-path)
+
 fish_config prompt list | string match -r '^(?:acidhub|disco|nim)$'
 # CHECK: acidhub
 # CHECK: disco
@@ -218,5 +220,31 @@ echo >$__fish_config_dir/themes/custom-from-userconf.theme \
     # CHECK: $fish_color_normal[1]: |normal|
 }
 
+{
+    echo >$__fish_config_dir/conf.d/fish_frozen_theme.fish "\
+set --global fish_color_command 0a0a0a
+set --global fish_color_option 0b0b0b"
+    echo >$__fish_config_dir/themes/from-cli.theme "\
+[light]
+fish_color_command black
+fish_color_param 0c0c0c
+[dark]
+fish_color_command white
+fish_color_param c0c0c0"
+    $fish -c '
+        fish_config theme choose from-cli
+        echo $fish_color_command
+        # CHECK: --theme=from-cli
+        echo $fish_color_option
+        # CHECK: 0b0b0b
+        echo $fish_color_param
+        # CHECK: --theme=from-cli
+        echo yes | fish_config theme save from-cli
+        # CHECKERR: fish_config theme save: error: $fish_terminal_color_theme not yet initialized
+        and echo assertion failure
+    '
+    rm -f $__fish_config_dir/conf.d/fish_frozen_theme.fish
+}
+
 fish_config theme dump badarg
 # CHECKERR: Too many arguments