diff --git a/packages/opencode/src/cli/cmd/tui/routes/session/permission.tsx b/packages/opencode/src/cli/cmd/tui/routes/session/permission.tsx
index c2cd4d17d9c..667761cd890 100644
--- a/packages/opencode/src/cli/cmd/tui/routes/session/permission.tsx
+++ b/packages/opencode/src/cli/cmd/tui/routes/session/permission.tsx
@@ -16,6 +16,7 @@ import { Locale } from "@/util/locale"
 import { Global } from "@/global"
 import { useDialog } from "../../ui/dialog"
 import { useTuiConfig } from "../../context/tui-config"
+import { ConfigProtection } from "@/kilocode/permission/config-paths" // kilocode_change
 
 type PermissionStage = "permission" | "always" | "reject"
 
@@ -428,12 +429,18 @@ export function PermissionPrompt(props: { request: PermissionRequest }) {
             </box>
           )
 
+          // kilocode_change start — hide "Always allow" for config file edits
+          const options: Record<string, string> = props.request.metadata?.[ConfigProtection.DISABLE_ALWAYS_KEY]
+            ? { once: "Allow once", reject: "Reject" }
+            : { once: "Allow once", always: "Allow always", reject: "Reject" }
+          // kilocode_change end
+
           const body = (
             <Prompt
               title="Permission required"
               header={header()}
               body={current.body}
-              options={{ once: "Allow once", always: "Allow always", reject: "Reject" }}
+              options={options}
               escapeKey="reject"
               fullscreen
               onSelect={(option) => {
diff --git a/packages/opencode/src/kilocode/permission/config-paths.ts b/packages/opencode/src/kilocode/permission/config-paths.ts
new file mode 100644
index 00000000000..facd70987ca
--- /dev/null
+++ b/packages/opencode/src/kilocode/permission/config-paths.ts
@@ -0,0 +1,129 @@
+import path from "path"
+import { Global } from "@/global"
+import { KilocodePaths } from "@/kilocode/paths"
+
+export namespace ConfigProtection {
+  /**
+   * Config directory prefixes (relative paths, forward-slash normalized).
+   * Matches .kilo/, .kilocode/, .opencode/ at any depth within the project.
+   */
+  const CONFIG_DIRS = [".kilo/", ".kilocode/", ".opencode/"]
+
+  /**
+   * Subdirectories under CONFIG_DIRS that are NOT config files (e.g. plan files).
+   * Paths under these subdirs are exempt from config protection.
+   */
+  const EXCLUDED_SUBDIRS = ["plans/"]
+
+  /**
+   * Root-level config files that must be protected.
+   * Matched only when the relative path has no directory component.
+   */
+  const CONFIG_ROOT_FILES = new Set(["kilo.json", "kilo.jsonc", "opencode.json", "opencode.jsonc", "AGENTS.md"])
+
+  /** Metadata key used to signal the UI to hide the "Allow always" option. */
+  export const DISABLE_ALWAYS_KEY = "disableAlways" as const
+
+  function normalize(p: string): string {
+    return path.posix.normalize(p.replaceAll("\\", "/"))
+  }
+
+  /** Return the remainder after the config dir prefix, or undefined if excluded. */
+  function excluded(remainder: string): boolean {
+    return EXCLUDED_SUBDIRS.some((sub) => remainder.startsWith(sub))
+  }
+
+  /** Check if a project-relative path points to a config file or directory. */
+  export function isRelative(pattern: string): boolean {
+    const normalized = normalize(pattern)
+    for (const dir of CONFIG_DIRS) {
+      const bare = dir.slice(0, -1) // e.g. ".kilo"
+      // Match at root (e.g. ".kilo/foo") or nested (e.g. "packages/sub/.kilo/foo")
+      if (normalized === bare || normalized.endsWith("/" + bare)) return true
+      if (normalized.startsWith(dir)) {
+        if (excluded(normalized.slice(dir.length))) continue
+        return true
+      }
+      const nested = normalized.indexOf("/" + dir)
+      if (nested !== -1) {
+        if (excluded(normalized.slice(nested + 1 + dir.length))) continue
+        return true
+      }
+    }
+    return CONFIG_ROOT_FILES.has(normalized)
+  }
+
+  /** Check if `child` is equal to or nested inside `parent`. */
+  function within(child: string, parent: string): boolean {
+    return child === parent || child.startsWith(parent + path.sep)
+  }
+
+  /** Check if an absolute path is inside a known CLI config directory. */
+  export function isAbsolute(filepath: string): boolean {
+    const resolved = path.resolve(filepath)
+
+    // ~/.config/kilo/ (XDG config)
+    if (within(resolved, path.resolve(Global.Path.config))) return true
+
+    // ~/.kilo/ and ~/.kilocode/ (legacy global dirs)
+    for (const dir of KilocodePaths.globalDirs()) {
+      if (within(resolved, path.resolve(dir))) return true
+    }
+
+    return false
+  }
+
+  /** Check a single path (absolute or relative) against config protection. */
+  function protected_(p: string): boolean {
+    return path.isAbsolute(p) ? isAbsolute(p) : isRelative(p)
+  }
+
+  /**
+   * Determine if a permission request targets config files.
+   * Checks `edit` and `external_directory` permissions — read access is not restricted.
+   */
+  export function isRequest(request: {
+    permission: string
+    patterns: string[]
+    metadata?: Record<string, any>
+  }): boolean {
+    // external_directory patterns are absolute globs like "/Users/alex/.config/kilo/*"
+    if (request.permission === "external_directory") {
+      for (const pattern of request.patterns) {
+        const dir = pattern.replace(/\/\*$/, "")
+        if (isAbsolute(dir)) return true
+      }
+      return false
+    }
+
+    if (request.permission !== "edit") return false
+
+    // Check patterns — handle both relative and absolute
+    for (const pattern of request.patterns) {
+      if (protected_(pattern)) return true
+    }
+
+    // Check metadata.filepath (absolute for edit, comma-joined relative for apply_patch)
+    const fp = request.metadata?.filepath
+    if (typeof fp === "string") {
+      // apply_patch joins relative paths with ", "
+      const parts = fp.includes(", ") ? fp.split(", ") : [fp]
+      for (const part of parts) {
+        if (protected_(part)) return true
+      }
+    }
+
+    // Check metadata.files[] (apply_patch file objects with absolute filePath/movePath)
+    const files = request.metadata?.files
+    if (Array.isArray(files)) {
+      for (const file of files) {
+        for (const key of ["filePath", "movePath"] as const) {
+          const val = file?.[key]
+          if (typeof val === "string" && protected_(val)) return true
+        }
+      }
+    }
+
+    return false
+  }
+}
diff --git a/packages/opencode/src/kilocode/permission/drain.ts b/packages/opencode/src/kilocode/permission/drain.ts
index 608932a4f0b..cfd6949c45d 100644
--- a/packages/opencode/src/kilocode/permission/drain.ts
+++ b/packages/opencode/src/kilocode/permission/drain.ts
@@ -1,6 +1,7 @@
 import { Bus } from "@/bus"
 import { Wildcard } from "@/util/wildcard"
 import type { PermissionNext } from "@/permission/next"
+import { ConfigProtection } from "@/kilocode/permission/config-paths"
 
 /**
  * Auto-resolve pending permissions now fully covered by approved or denied rules.
@@ -25,6 +26,8 @@ export async function drainCovered(
 ) {
   for (const [id, entry] of Object.entries(pending)) {
     if (id === exclude) continue
+    // Never auto-resolve config file edit permissions
+    if (ConfigProtection.isRequest(entry.info)) continue
     const actions = entry.info.patterns.map((pattern) =>
       evaluate(entry.info.permission, pattern, entry.ruleset, approved),
     )
diff --git a/packages/opencode/src/permission/next.ts b/packages/opencode/src/permission/next.ts
index 5534572da26..b68fafd1f8a 100644
--- a/packages/opencode/src/permission/next.ts
+++ b/packages/opencode/src/permission/next.ts
@@ -9,6 +9,7 @@ import { fn } from "@/util/fn"
 import { Log } from "@/util/log"
 import { Wildcard } from "@/util/wildcard"
 import { drainCovered } from "@/kilocode/permission/drain" // kilocode_change
+import { ConfigProtection } from "@/kilocode/permission/config-paths" // kilocode_change
 import os from "os"
 import z from "zod"
 
@@ -188,18 +189,27 @@ export namespace PermissionNext {
     async (input) => {
       const s = await state()
       const { ruleset, ...request } = input
+      // kilocode_change start — force "ask" for config file edits
+      const protected_ = ConfigProtection.isRequest(request)
+      // kilocode_change end
       for (const pattern of request.patterns ?? []) {
         const rule = evaluate(request.permission, pattern, ruleset, s.approved)
         log.info("evaluated", { permission: request.permission, pattern, action: rule })
         if (rule.action === "deny")
           throw new DeniedError(ruleset.filter((r) => Wildcard.match(request.permission, r.permission)))
-        if (rule.action === "ask") {
+        // kilocode_change start — override "allow" to "ask" for config paths
+        if (rule.action === "ask" || (rule.action === "allow" && protected_)) {
           const id = input.id ?? Identifier.ascending("permission")
           return new Promise<void>((resolve, reject) => {
             const info: Request = {
               id,
               ...request,
+              metadata: {
+                ...request.metadata,
+                ...(protected_ ? { [ConfigProtection.DISABLE_ALWAYS_KEY]: true } : {}),
+              },
             }
+            // kilocode_change end
             s.pending[id] = {
               info,
               ruleset, // kilocode_change
@@ -227,6 +237,10 @@ export namespace PermissionNext {
       const existing = s.pending[input.requestID]
       if (!existing) throw new NotFoundError({ message: `Permission request ${input.requestID} not found` })
 
+      // kilocode_change start — skip rule persistence for config file edits
+      if (ConfigProtection.isRequest(existing.info)) return
+      // kilocode_change end
+
       // Combine metadata.rules (bash hierarchy) and always (all tools).
       // Set preserves insertion order and deduplicates.
       const validRules = new Set([...(existing.info.metadata?.rules ?? []), ...existing.info.always])
@@ -289,6 +303,13 @@ export namespace PermissionNext {
         return
       }
       if (input.reply === "always") {
+        // kilocode_change start — downgrade "always" to "once" for config file edits
+        if (ConfigProtection.isRequest(existing.info)) {
+          existing.resolve()
+          return
+        }
+        // kilocode_change end
+
         for (const pattern of existing.info.always) {
           s.approved.push({
             permission: existing.info.permission,