diff --git a/modules/programs/codex.nix b/modules/programs/codex.nix
index 14662db1..c238c144 100644
--- a/modules/programs/codex.nix
+++ b/modules/programs/codex.nix
@@ -99,12 +99,14 @@ in
 
         If an attribute set is used, the attribute name becomes the skill directory name,
         and the value is either:
-        - Inline content as a string (creates {file}`<skills-dir>/<name>/SKILL.md`)
-        - A path to a file (creates {file}`<skills-dir>/<name>/SKILL.md`)
-        - A path to a directory (creates {file}`<skills-dir>/<name>/` with all files)
+        - Inline content as a string (creates a generated skill directory at {file}`<skills-dir>/<name>/`)
+        - A path to a file (creates a generated skill directory at {file}`<skills-dir>/<name>/`)
+        - A path to a directory (symlinks {file}`<skills-dir>/<name>/` to that directory)
 
         If a path is used, it is expected to contain one folder per skill name, each
-        containing a {file}`SKILL.md`. The directory is symlinked to {file}`<skills-dir>/`.
+        containing a {file}`SKILL.md`. Each top-level skill entry is symlinked into
+        {file}`<skills-dir>/`, leaving {file}`<skills-dir>/` itself as a normal
+        directory so unmanaged skills can coexist.
 
         The skills target directory depends on Codex version:
         - {file}`~/.agents/skills` for Codex >= 0.94.0
@@ -145,6 +147,30 @@ in
       configFileName = if isTomlConfig then "config.toml" else "config.yaml";
       skillsDir = if isAgentsSkillsSupported then ".agents/skills" else "${configDir}/skills";
 
+      # TODO: Remove this workaround once Codex supports symlinked SKILL.md
+      # files again. Upstream only supports symlinking the containing skill
+      # directory today: https://github.com/openai/codex/issues/10470
+      mkSkillDir =
+        content:
+        pkgs.writeTextDir "SKILL.md" (if lib.isPath content then builtins.readFile content else content);
+      skillSources =
+        if builtins.isAttrs cfg.skills then
+          cfg.skills
+        else if lib.isPath cfg.skills && lib.pathIsDirectory cfg.skills then
+          lib.mapAttrs (name: _type: cfg.skills + "/${name}") (builtins.readDir cfg.skills)
+        else
+          { };
+      mkSkillEntry =
+        name: content:
+        if lib.isPath content && lib.pathIsDirectory content then
+          lib.nameValuePair "${skillsDir}/${name}" {
+            source = content;
+          }
+        else
+          lib.nameValuePair "${skillsDir}/${name}" {
+            source = mkSkillDir content;
+          };
+
       transformedMcpServers = lib.optionalAttrs (cfg.enableMcpIntegration && config.programs.mcp.enable) (
         lib.mapAttrs (
           _name: server:
@@ -189,23 +215,8 @@ in
           "${configDir}/AGENTS.md" = lib.mkIf (cfg.custom-instructions != "") {
             text = cfg.custom-instructions;
           };
-          "${skillsDir}" = lib.mkIf (lib.isPath cfg.skills) {
-            source = cfg.skills;
-            recursive = true;
-          };
         }
-        // (lib.mapAttrs' (
-          name: content:
-          if lib.isPath content && lib.pathIsDirectory content then
-            lib.nameValuePair "${skillsDir}/${name}" {
-              source = content;
-              recursive = true;
-            }
-          else
-            lib.nameValuePair "${skillsDir}/${name}/SKILL.md" (
-              if lib.isPath content then { source = content; } else { text = content; }
-            )
-        ) (if builtins.isAttrs cfg.skills then cfg.skills else { }));
+        // lib.mapAttrs' mkSkillEntry skillSources;
 
         sessionVariables = mkIf useXdgDirectories {
           CODEX_HOME = "${config.xdg.configHome}/codex";
diff --git a/tests/modules/programs/codex/skills-dir.nix b/tests/modules/programs/codex/skills-dir.nix
index eaa48d53..27dca73e 100644
--- a/tests/modules/programs/codex/skills-dir.nix
+++ b/tests/modules/programs/codex/skills-dir.nix
@@ -13,7 +13,14 @@ in
   };
 
   nmt.script = ''
+    if [[ -L home-files/.agents/skills ]]; then
+      fail "Expected home-files/.agents/skills to remain a normal directory so unmanaged skills can coexist."
+    fi
+    assertLinkExists home-files/.agents/skills/skill-one
     assertFileExists home-files/.agents/skills/skill-one/SKILL.md
+    if [[ -L home-files/.agents/skills/skill-one/SKILL.md ]]; then
+      fail "Expected home-files/.agents/skills/skill-one/SKILL.md to be a regular file inside a symlinked skill directory."
+    fi
     assertFileContent home-files/.agents/skills/skill-one/SKILL.md \
       ${./skills-dir/skill-one/SKILL.md}
   '';
diff --git a/tests/modules/programs/codex/skills-inline-legacy-path.nix b/tests/modules/programs/codex/skills-inline-legacy-path.nix
index 5030a40f..b9bb27c6 100644
--- a/tests/modules/programs/codex/skills-inline-legacy-path.nix
+++ b/tests/modules/programs/codex/skills-inline-legacy-path.nix
@@ -17,7 +17,14 @@ in
   };
 
   nmt.script = ''
+    if [[ -L home-files/.codex/skills ]]; then
+      fail "Expected home-files/.codex/skills to remain a normal directory so unmanaged skills can coexist."
+    fi
+    assertLinkExists home-files/.codex/skills/inline-skill
     assertFileExists home-files/.codex/skills/inline-skill/SKILL.md
+    if [[ -L home-files/.codex/skills/inline-skill/SKILL.md ]]; then
+      fail "Expected home-files/.codex/skills/inline-skill/SKILL.md to be a regular file inside a symlinked skill directory."
+    fi
     assertFileContent home-files/.codex/skills/inline-skill/SKILL.md \
       ${builtins.toFile "expected-inline-skill.md" ''
         # Inline Skill
diff --git a/tests/modules/programs/codex/skills-inline-null-package.nix b/tests/modules/programs/codex/skills-inline-null-package.nix
index c3bc019f..63e4f469 100644
--- a/tests/modules/programs/codex/skills-inline-null-package.nix
+++ b/tests/modules/programs/codex/skills-inline-null-package.nix
@@ -10,7 +10,11 @@
   };
 
   nmt.script = ''
+    assertLinkExists home-files/.agents/skills/inline-skill
     assertFileExists home-files/.agents/skills/inline-skill/SKILL.md
+    if [[ -L home-files/.agents/skills/inline-skill/SKILL.md ]]; then
+      fail "Expected home-files/.agents/skills/inline-skill/SKILL.md to be a regular file inside a symlinked skill directory."
+    fi
     assertFileContent home-files/.agents/skills/inline-skill/SKILL.md \
       ${builtins.toFile "expected-inline-skill.md" ''
         # Inline Skill
diff --git a/tests/modules/programs/codex/skills-inline.nix b/tests/modules/programs/codex/skills-inline.nix
index 80ad05de..8f18227d 100644
--- a/tests/modules/programs/codex/skills-inline.nix
+++ b/tests/modules/programs/codex/skills-inline.nix
@@ -22,15 +22,34 @@ in
     skills = {
       inline-skill = inlineSkill;
       file-skill = ./skill-file.md;
+      dir-skill = ./skills-dir/skill-one;
     };
   };
 
   nmt.script = ''
+    if [[ -L home-files/.agents/skills ]]; then
+      fail "Expected home-files/.agents/skills to remain a normal directory so unmanaged skills can coexist."
+    fi
+    assertLinkExists home-files/.agents/skills/inline-skill
     assertFileExists home-files/.agents/skills/inline-skill/SKILL.md
+    if [[ -L home-files/.agents/skills/inline-skill/SKILL.md ]]; then
+      fail "Expected home-files/.agents/skills/inline-skill/SKILL.md to be a regular file inside a symlinked skill directory."
+    fi
     assertFileContent home-files/.agents/skills/inline-skill/SKILL.md \
       ${builtins.toFile "expected-inline-skill.md" inlineSkill}
+    assertLinkExists home-files/.agents/skills/file-skill
     assertFileExists home-files/.agents/skills/file-skill/SKILL.md
+    if [[ -L home-files/.agents/skills/file-skill/SKILL.md ]]; then
+      fail "Expected home-files/.agents/skills/file-skill/SKILL.md to be a regular file inside a symlinked skill directory."
+    fi
     assertFileContent home-files/.agents/skills/file-skill/SKILL.md \
       ${./skill-file.md}
+    assertLinkExists home-files/.agents/skills/dir-skill
+    assertFileExists home-files/.agents/skills/dir-skill/SKILL.md
+    if [[ -L home-files/.agents/skills/dir-skill/SKILL.md ]]; then
+      fail "Expected home-files/.agents/skills/dir-skill/SKILL.md to be a regular file inside a symlinked skill directory."
+    fi
+    assertFileContent home-files/.agents/skills/dir-skill/SKILL.md \
+      ${./skills-dir/skill-one/SKILL.md}
   '';
 }