diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 28b9e6769..dbe3701aa 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,7 +13,7 @@ fish 4.3.0 (released December 28, 2025)
 
 Deprecations and removed features
 ---------------------------------
-- fish no longer sets :ref:`universal variables <variables-universal>` by default, making the configuration easier to understand.
+- fish no longer sets user-facing :ref:`universal variables <variables-universal>` by default, making the configuration easier to understand.
   Specifically, the ``fish_color_*``, ``fish_pager_color_*`` and ``fish_key_bindings`` variables are now set in the global scope by default.
   After upgrading to 4.3.0, fish will (once and never again) migrate these universals to globals set at startup in the
   ``~/.config/fish/conf.d/fish_frozen_theme.fish`` and
diff --git a/share/config.fish b/share/config.fish
index bc48cc01d..4ced2cdff 100644
--- a/share/config.fish
+++ b/share/config.fish
@@ -205,7 +205,7 @@ if command -q kill
 end
 
 if status is-interactive
-    __fish_theme_migrate
+    __fish_migrate
 end
 fish_config theme choose default --no-override
 
diff --git a/share/functions/__fish_config_interactive.fish b/share/functions/__fish_config_interactive.fish
index e77470e15..f482770f5 100644
--- a/share/functions/__fish_config_interactive.fish
+++ b/share/functions/__fish_config_interactive.fish
@@ -6,15 +6,6 @@
 #
 function __fish_config_interactive -d "Initializations that should be performed when entering interactive mode"
     functions -e __fish_config_interactive
-    # Create empty configuration directores if they do not already exist
-    test -e $__fish_config_dir/completions/ -a -e $__fish_config_dir/conf.d/ -a -e $__fish_config_dir/functions/ ||
-        mkdir -p $__fish_config_dir/{completions, conf.d, functions}
-
-    # Create config.fish with some boilerplate if it does not exist
-    test -e $__fish_config_dir/config.fish || echo "\
-if status is-interactive
-# Commands to run in interactive sessions can go here
-end" >$__fish_config_dir/config.fish
 
     set -g __fish_active_key_bindings
 
diff --git a/share/functions/__fish_theme_migrate.fish b/share/functions/__fish_migrate.fish
similarity index 85%
rename from share/functions/__fish_theme_migrate.fish
rename to share/functions/__fish_migrate.fish
index 3e3e3c58a..51b74db67 100644
--- a/share/functions/__fish_theme_migrate.fish
+++ b/share/functions/__fish_migrate.fish
@@ -1,9 +1,27 @@
 # localization: skip(private)
-function __fish_theme_migrate
-    functions -e __fish_theme_migrate
+function __fish_migrate
+    functions -e __fish_migrate
+
+    set -l migration_version 4300
 
     # Maybe migrate.
-    if not set -q __fish_initialized || test $__fish_initialized -ge 4300
+    if set -q __fish_initialized && test $__fish_initialized -ge $migration_version
+        return
+    end
+
+    # Create empty configuration directores if they do not already exist
+    test -e $__fish_config_dir/completions/ -a -e $__fish_config_dir/conf.d/ -a -e $__fish_config_dir/functions/ ||
+        mkdir -p $__fish_config_dir/{completions, conf.d, functions}
+
+    # Create config.fish with some boilerplate if it does not exist
+    test -e $__fish_config_dir/config.fish || echo "\
+if status is-interactive
+# Commands to run in interactive sessions can go here
+end" >$__fish_config_dir/config.fish
+
+    set -l mark_migration_done set -U __fish_initialized $migration_version
+    if not set -q __fish_initialized
+        $mark_migration_done
         return
     end
 
@@ -22,7 +40,7 @@ function __fish_theme_migrate
             for varname in $theme_uvars
                 set -a theme_data "$(string escape -- $varname $$varname | string join " ")"
             end
-            __fish_theme_freeze __fish_theme_migrate $theme_data
+            __fish_theme_freeze __fish_migrate $theme_data
             set msg_suffix " by default."\n"  Migrated them to global variables set in $(set_color --underline)$(
                     __fish_unexpand_tilde $__fish_config_dir/conf.d/fish_frozen_theme.fish
                 )$(set_color normal)"
@@ -35,6 +53,7 @@ function __fish_theme_migrate
         set -l relative_filename conf.d/fish_frozen_key_bindings.fish
         set -l filename $__fish_config_dir/$relative_filename
         __fish_backup_config_files $relative_filename
+        mkdir -p -- (path dirname -- $filename)
         echo >$filename "\
 # This file was created by fish when upgrading to version 4.3, to migrate
 # the 'fish_key_bindings' variable from its old default scope (universal)
@@ -62,7 +81,7 @@ set --erase --universal fish_key_bindings"
             (set_color normal))
         source $__fish_config_dir/$relative_filename
     end
-    set -U __fish_initialized 4300
+    $mark_migration_done
     if $removing_uvars
         echo -s (set_color --bold) 'fish:' (set_color normal) " upgraded to version 4.3:"
         string join \n -- $msg
diff --git a/share/functions/__fish_theme_freeze.fish b/share/functions/__fish_theme_freeze.fish
index 4b6b8355c..1c8b5925c 100644
--- a/share/functions/__fish_theme_freeze.fish
+++ b/share/functions/__fish_theme_freeze.fish
@@ -9,8 +9,9 @@ function __fish_theme_freeze
     __fish_data_with_file help_sections $(command -v grep) -Fxq $help_section
     or echo "fish: internal error: missing help section '$help_section'"
 
+    mkdir -p -- (path dirname -- $__fish_config_dir/conf.d)
     printf >$__fish_config_dir/$relative_path %s\n \
-        $(test $data_source = __fish_theme_migrate &&
+        $(test $data_source = __fish_migrate &&
             echo "\
 # This file was created by fish when upgrading to version 4.3, to migrate
 # theme variables from universal to global scope.") \
@@ -21,7 +22,7 @@ function __fish_theme_freeze
 # or
 #     man fish-interactive | less +/^SYNTAX.HIGHLIGHTING
 # for appropriate commands to add to ~/.config/fish/config.fish instead." \
-        $(test $data_source = __fish_theme_migrate &&
+        $(test $data_source = __fish_migrate &&
             echo '# See also the release notes for fish 4.3.0 (run `help relnotes`).') \
         "" \
         'set --global '$theme_data
diff --git a/tests/checks/__fish_theme_migrate.fish b/tests/checks/__fish_migrate.fish
similarity index 96%
rename from tests/checks/__fish_theme_migrate.fish
rename to tests/checks/__fish_migrate.fish
index 0139bf587..923a7c2a7 100644
--- a/tests/checks/__fish_theme_migrate.fish
+++ b/tests/checks/__fish_migrate.fish
@@ -30,7 +30,7 @@ echo no default universal variables
     # CHECK: ok
 
     provoke-migration
-    $fish -c __fish_theme_migrate
+    $fish -c __fish_migrate
     # CHECK: {{\x1b\[1m}}fish:{{\x1b\[m}} {{upgraded.*}}
     # CHECK: {{.*Color.*no.longer.*universal.*}}
     # CHECK: Migrated {{.*}} {{\S*}}/xdg_config_home/fish/conf.d/fish_frozen_theme.fish{{\x1b\[m}}
@@ -49,7 +49,7 @@ echo no default universal variables
     # But the migration is only done once, in case the user really wants these as universals.
     set -U fish_color_autosuggestion 8e8e8e
     $fish -c '
-        __fish_theme_migrate
+        __fish_migrate
         set -eg fish_color_autosuggestion
         echo $fish_color_autosuggestion
         # CHECK: 8e8e8e
@@ -63,7 +63,7 @@ echo no default universal variables
     echo yes | fish_config theme save default
     fake-old-uvars
     provoke-migration
-    $fish -c __fish_theme_migrate
+    $fish -c __fish_migrate
     # CHECK: {{\x1b\[1m}}fish:{{\x1b\[m}} {{upgraded.*}}
     # CHECK: {{.*Color.*no.longer.*universal.*}}
     # CHECK: {{.*restart.*}}
@@ -80,7 +80,7 @@ echo no default universal variables
     $fish -c '
         set -g fish_color_autosuggestion red
         set -g fish_color_command green --theme=default
-        __fish_theme_migrate
+        __fish_migrate
         for cmd in "" "__fish_color_theme=unknown __fish_apply_theme"
             eval $cmd
             echo fish_color_autosuggestion $fish_color_autosuggestion
@@ -98,7 +98,7 @@ echo no default universal variables
 {
     set -U fish_key_bindings fish_vi_key_bindings
     provoke-migration
-    $fish -c __fish_theme_migrate
+    $fish -c __fish_migrate
     # CHECK: {{\x1b\[1m}}fish:{{\x1b\[m}} {{upgraded.*}}
     # CHECK: {{.*fish_key_bindings.*no.longer.*universal.*}}
     # CHECK: Migrated {{.*}} {{\S*}}/xdg_config_home/fish/conf.d/fish_frozen_key_bindings.fish{{\x1b\[m}}
diff --git a/tests/checks/command-not-found.fish b/tests/checks/command-not-found.fish
index c5b07ab16..151c21e52 100644
--- a/tests/checks/command-not-found.fish
+++ b/tests/checks/command-not-found.fish
@@ -1,4 +1,5 @@
 #RUN: fish=%fish %fish %s
+__fish_migrate # make sure the interactive fish doesn't need mkdir in PATH
 set -g PATH
 $fish -c "nonexistent-command-1234 banana rama"
 #CHECKERR: fish: Unknown command: nonexistent-command-1234