diff --git a/packages/opencode/src/config/paths.ts b/packages/opencode/src/config/paths.ts
index e9f2241776..b67c96416e 100644
--- a/packages/opencode/src/config/paths.ts
+++ b/packages/opencode/src/config/paths.ts
@@ -77,17 +77,27 @@ export namespace ConfigPaths {
       return process.env[varName] || ""
     })
 
-    const fileMatches = text.match(/\{file:[^}]+\}/g)
-    if (!fileMatches) return text
+    const fileMatches = Array.from(text.matchAll(/\{file:[^}]+\}/g))
+    if (!fileMatches.length) return text
 
     const configDir = path.dirname(configFilepath)
-    const lines = text.split("\n")
+    let out = ""
+    let cursor = 0
 
     for (const match of fileMatches) {
-      const lineIndex = lines.findIndex((line) => line.includes(match))
-      if (lineIndex !== -1 && lines[lineIndex].trim().startsWith("//")) continue
+      const token = match[0]
+      const index = match.index!
+      out += text.slice(cursor, index)
 
-      let filePath = match.replace(/^\{file:/, "").replace(/\}$/, "")
+      const lineStart = text.lastIndexOf("\n", index - 1) + 1
+      const prefix = text.slice(lineStart, index).trimStart()
+      if (prefix.startsWith("//")) {
+        out += token
+        cursor = index + token.length
+        continue
+      }
+
+      let filePath = token.replace(/^\{file:/, "").replace(/\}$/, "")
       if (filePath.startsWith("~/")) {
         filePath = path.join(os.homedir(), filePath.slice(2))
       }
@@ -99,7 +109,7 @@ export namespace ConfigPaths {
           .catch((error) => {
             if (missing === "empty") return ""
 
-            const errMsg = `bad file reference: "${match}"`
+            const errMsg = `bad file reference: "${token}"`
             if (error.code === "ENOENT") {
               throw new InvalidError(
                 {
@@ -113,10 +123,12 @@ export namespace ConfigPaths {
           })
       ).trim()
 
-      text = text.replace(match, () => JSON.stringify(fileContent).slice(1, -1))
+      out += JSON.stringify(fileContent).slice(1, -1)
+      cursor = index + token.length
     }
 
-    return text
+    out += text.slice(cursor)
+    return out
   }
 
   /** Substitute and parse JSONC text, throwing JsonError on syntax errors. */
diff --git a/packages/opencode/test/config/tui.test.ts b/packages/opencode/test/config/tui.test.ts
index 2a98853dfb..0f4e9d3b1e 100644
--- a/packages/opencode/test/config/tui.test.ts
+++ b/packages/opencode/test/config/tui.test.ts
@@ -384,6 +384,29 @@ test("applies env and file substitutions in tui.json", async () => {
   }
 })
 
+test("applies file substitutions when first identical token is in a commented line", async () => {
+  await using tmp = await tmpdir({
+    init: async (dir) => {
+      await Bun.write(path.join(dir, "theme.txt"), "resolved-theme")
+      await Bun.write(
+        path.join(dir, "tui.jsonc"),
+        `{
+  // "theme": "{file:theme.txt}",
+  "theme": "{file:theme.txt}"
+}`,
+      )
+    },
+  })
+
+  await Instance.provide({
+    directory: tmp.path,
+    fn: async () => {
+      const config = await TuiConfig.get()
+      expect(config.theme).toBe("resolved-theme")
+    },
+  })
+})
+
 test("loads managed tui config and gives it highest precedence", async () => {
   await using tmp = await tmpdir({
     init: async (dir) => {