diff --git a/src/cli.ts b/src/cli.ts
index 686c7d5..f44caac 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -4,10 +4,12 @@ import { join } from "node:path";
 import { homedir } from "node:os";
 import * as readline from "node:readline";
 import { startAuthFlow, clearCredentials, loadCredentials, CREDENTIALS_FILE } from "./services/auth.js";
-import { CONFIG, CONFIG_FILE, SUPERMEMORY_API_KEY, getApiBaseUrl, isConfigured, writeInstallDefaults } from "./config.js";
+import { CONFIG, CONFIG_FILE, SUPERMEMORY_API_KEY, getApiBaseUrl, isConfigured } from "./config.js";
 import { SupermemoryClient } from "./services/client.js";
 import { getTags } from "./services/tags.js";
+import { stripJsoncComments } from "./services/jsonc.js";
 import {
+  applyInstallDefaults,
   editOpenCodeConfig,
   editOpenCodeTuiConfig,
   readOpenCodeRegistration,
@@ -408,6 +410,16 @@ function disableAutoCompactHook(): boolean {
   }
 }
 
+function writeInstallDefaults(isExistingInstall: boolean): void {
+  const raw = isExistingInstall ? readFileSync(DEFAULT_CONFIG_FILE, "utf-8") : "";
+  const next = applyInstallDefaults(raw, isExistingInstall);
+  if (next === null) {
+    console.warn(`⚠ Could not parse ${DEFAULT_CONFIG_FILE}; left it unchanged.`);
+  } else if (next !== raw) {
+    writeFileSync(DEFAULT_CONFIG_FILE, next);
+  }
+}
+
 interface InstallOptions {
   tui: boolean;
   disableAutoCompact: boolean;
@@ -535,7 +547,7 @@ function maskKey(key: string | undefined): string {
 function getConfiguredApiKeyFromFile(): string | undefined {
   try {
     if (!existsSync(DEFAULT_CONFIG_FILE)) return undefined;
-    const parsed = JSON.parse(readFileSync(DEFAULT_CONFIG_FILE, "utf-8")) as { apiKey?: string };
+    const parsed = JSON.parse(stripJsoncComments(readFileSync(DEFAULT_CONFIG_FILE, "utf-8"))) as { apiKey?: string };
     return parsed.apiKey;
   } catch {
     return undefined;
diff --git a/src/config.ts b/src/config.ts
index b342f7b..338b8ef 100644
--- a/src/config.ts
+++ b/src/config.ts
@@ -1,4 +1,4 @@
-import { existsSync, readFileSync, writeFileSync } from "node:fs";
+import { existsSync, readFileSync } from "node:fs";
 import { join } from "node:path";
 import { homedir } from "node:os";
 import { stripJsoncComments } from "./services/jsonc.js";
@@ -118,22 +118,22 @@ function resolveRecallMode(): RecallMode {
   return DEFAULTS.recallMode;
 }
 
-function loadRawConfig(): { config: SupermemoryConfig; existed: boolean } {
+function loadRawConfig(): { config: SupermemoryConfig; existed: boolean; path?: string } {
   for (const path of CONFIG_FILES) {
     if (existsSync(path)) {
       try {
         const content = readFileSync(path, "utf-8");
         const json = stripJsoncComments(content);
-        return { config: JSON.parse(json) as SupermemoryConfig, existed: true };
+        return { config: JSON.parse(json) as SupermemoryConfig, existed: true, path };
       } catch {
-        return { config: {}, existed: true };
+        return { config: {}, existed: true, path };
       }
     }
   }
   return { config: {}, existed: false };
 }
 
-const { config: fileConfig, existed: configExisted } = loadRawConfig();
+const { config: fileConfig, existed: configExisted, path: loadedConfigFile } = loadRawConfig();
 
 function getApiKey(): string | undefined {
   if (process.env.SUPERMEMORY_API_KEY) return process.env.SUPERMEMORY_API_KEY;
@@ -172,8 +172,8 @@ export function getApiBaseUrl(): string {
   return normalized;
 }
 
-export const CONFIG_FILE = CONFIG_FILES[1];
-const DEFAULT_CONFIG_FILE = CONFIG_FILE ?? join(CONFIG_DIR, "supermemory.json");
+/** The file the config was loaded from, or where a new one should be created. */
+export const CONFIG_FILE = loadedConfigFile ?? CONFIG_FILES[1];
 
 export const CONFIG = {
   similarityThreshold: fileConfig.similarityThreshold ?? DEFAULTS.similarityThreshold,
@@ -218,15 +218,3 @@ export function getRecallConfig(): {
     mode: CONFIG.recallMode,
   };
 }
-
-export function writeInstallDefaults(isExistingInstall: boolean): void {
-  const current = loadRawConfig().config;
-  const next: SupermemoryConfig = { ...current };
-  if (isExistingInstall) {
-    if (next.captureEveryNTurns === undefined) next.captureEveryNTurns = 3;
-  } else {
-    next.recallMode = "direct";
-    next.captureEveryNTurns = 0;
-  }
-  writeFileSync(DEFAULT_CONFIG_FILE, JSON.stringify(next, null, 2));
-}
diff --git a/src/services/opencode-config.test.ts b/src/services/opencode-config.test.ts
index 79b1a48..40dea19 100644
--- a/src/services/opencode-config.test.ts
+++ b/src/services/opencode-config.test.ts
@@ -1,6 +1,7 @@
 import { describe, expect, test } from "bun:test";
 
 import {
+  applyInstallDefaults,
   editOpenCodeConfig,
   editOpenCodeTuiConfig,
   readOpenCodeRegistration,
@@ -89,3 +90,36 @@ describe("OpenCode V1 TUI config editor", () => {
     expect(readOpenCodeTuiRegistration('{"plugin": ["other"]}')).toBe(false);
   });
 });
+
+describe("applyInstallDefaults", () => {
+  const jsonc = `{
+  // created per README
+  "apiKey": "sm_test",
+  "recallMode": "advisory"
+}
+`;
+
+  test("keeps comments and user settings in an existing jsonc config", () => {
+    const next = applyInstallDefaults(jsonc, true)!;
+
+    expect(next).toContain("// created per README");
+    expect(next).toContain('"recallMode": "advisory"');
+    expect(next).toContain('"captureEveryNTurns": 3');
+  });
+
+  test("leaves an existing capture cadence untouched", () => {
+    const content = `{ "captureEveryNTurns": 5 } // keep`;
+    expect(applyInstallDefaults(content, true)).toBe(content);
+  });
+
+  test("writes fresh-install defaults to an empty config", () => {
+    expect(JSON.parse(applyInstallDefaults("", false)!)).toEqual({
+      recallMode: "direct",
+      captureEveryNTurns: 0,
+    });
+  });
+
+  test("does not rewrite a config it cannot parse", () => {
+    expect(applyInstallDefaults(`{ "apiKey": `, true)).toBeNull();
+  });
+});
diff --git a/src/services/opencode-config.ts b/src/services/opencode-config.ts
index c486259..4ef2316 100644
--- a/src/services/opencode-config.ts
+++ b/src/services/opencode-config.ts
@@ -206,3 +206,28 @@ export function editOpenCodeConfig(rawContent: string): OpenCodeConfigEditResult
     warnings,
   };
 }
+
+/**
+ * Adds installer defaults to supermemory.json(c) without rewriting the rest of
+ * the file, so user comments survive. Returns null for content that is not a
+ * valid JSONC object, which should be left for the user to fix.
+ */
+export function applyInstallDefaults(rawContent: string, isExistingInstall: boolean): string | null {
+  const content = rawContent.trim() === "" ? "{}\n" : rawContent;
+  let config: JsonObject;
+  try {
+    config = parseOpenCodeConfig(content);
+  } catch {
+    return null;
+  }
+
+  const defaults: JsonObject = isExistingInstall
+    ? config.captureEveryNTurns === undefined ? { captureEveryNTurns: 3 } : {}
+    : { recallMode: "direct", captureEveryNTurns: 0 };
+
+  let next = content;
+  for (const [key, value] of Object.entries(defaults)) {
+    next = applyModification(next, [key], value);
+  }
+  return next;
+}