diff --git a/src/config/validation.ts b/src/config/validation.ts
index 6a869888d01..01c320414c2 100644
--- a/src/config/validation.ts
+++ b/src/config/validation.ts
@@ -766,7 +766,8 @@ function validateConfigObjectWithPluginsBase(
         schema: channelSchema,
         cacheKey: `channel:${trimmed}`,
         value: config.channels[trimmed],
-        applyDefaults: opts.applyDefaults,
+        applyDefaults: true, // Always apply defaults for AJV schema validation;
+        // writeConfigFile persists persistCandidate, not validated.config (#61841)
       });
       if (!result.ok) {
         for (const error of result.errors) {
@@ -957,7 +958,8 @@ function validateConfigObjectWithPluginsBase(
           schema: record.configSchema,
           cacheKey: record.schemaCacheKey ?? record.manifestPath ?? pluginId,
           value: entry?.config ?? {},
-          applyDefaults: opts.applyDefaults,
+          applyDefaults: true, // Always apply defaults for AJV schema validation;
+          // writeConfigFile persists persistCandidate, not validated.config (#61841)
         });
         if (!res.ok) {
           for (const error of res.errors) {