How to Fix When WordPress Scheduled Backups or Cron Jobs Fail Because of Conflicting Plugins — Cron Reset + Conflict Isolation That Restored Automation

Published On - December 9, 2025

Olivia Brown Blog

Automated backups and scheduled tasks (cron jobs) are the unseen workhorses of any serious WordPress site, quietly ensuring both data safety and operational reliability. But what happens when these automations mysteriously stop working? This article explores how conflicting plugins can silently disrupt core background processes in WordPress—delaying backups, halting emails, and derailing crucial site functions. We’ll delve into how to detect and fix this issue using a structured approach involving cron reset and conflict isolation.

TL;DR

If your WordPress scheduled backups or cron jobs are failing, the root cause is often a plugin conflict that disrupts WP-Cron events. The fix involves resetting your cron system and systematically deactivating plugins to isolate the culprit. Prioritize checking plugins that modify time-related features or performance. Once the conflict is identified and resolved, automation should be restored, ensuring your backups and scheduled tasks function reliably again.

Understanding the Problem: Symptoms of Failing Cron Jobs

WordPress uses a built-in mechanism called WP-Cron to handle scheduled tasks. These tasks can include:

  • Database and file backups
  • Scheduled posts and publication
  • Plugin-defined automations (e.g., cleanups, updates, email dispatches)

When cron jobs fail, the consequences can be subtle or severe. You may notice missed posts, unopened transactional emails, or, most critically for site owners, the failure of backup plugins like UpdraftPlus, BlogVault, or Jetpack to perform their scheduled backups.

Common symptoms include:

  • Repeated “missed schedule” errors in the WordPress dashboard
  • No recent backup entries in your backup plugin log
  • WP-Cron events not firing even after visits to public-facing pages

This kind of silent failure typically arises when a plugin hooks into or interferes with the WP-Cron engine. While the specific triggers may vary, plugin conflicts account for a vast number of these issues.

Step 1: Confirm the Issue is with WP-Cron

Before jumping to conflict isolation, you should first confirm that WP-Cron is indeed not working.

  1. Install a plugin like WP Crontrol. It gives access to all scheduled cron events.
  2. Go to Tools > Cron Events and check if schedules are pending or stuck.
  3. Try executing failing jobs manually and monitor if they succeed or log errors.

If timestamps appear outdated or the “Next Run” remains constant across different refreshes, your WP-Cron system is likely malfunctioning.

Additionally, if your site is low-traffic (no visitors to trigger WP-Cron), consider visiting your site yourself multiple times to manually invoke it or set a real system cron job to call wp-cron.php at regular intervals.

Step 2: Reset the Cron System

If cron events are obviously jammed or not scheduling properly even with plugins like UpdraftPlus or WP Mail SMTP, a full cron reset is warranted. This doesn’t mean resetting all WordPress settings; it refers specifically to clearing malformed or conflicting scheduled tasks and allowing them to repopulate.

Here’s how to do it safely:

  1. Make a full backup of your site manually (yes: ironic, since backup automation is broken!)
  2. Install and activate the WP Crontrol plugin.
  3. From Tools > Cron Events, identify and remove obviously out-of-place or broken jobs (e.g., tens of duplicate unscheduled jobs).
  4. Temporarily deactivate plugins that create their own cron jobs like caching toolkits, backup plugins, and email-loggers.
  5. Visit your site or force a cron run by accessing: https://yoursite.com/wp-cron.php?doing_wp_cron
  6. Re-enable your backup plugin and manually trigger a backup to regenerate fresh cron jobs.

This will help clear any corrupted schedule queue and re-align task triggers.

Step 3: Isolating the Conflicting Plugin

The most common culprits are plugins that either:

  • Override server-side cron behavior
  • Add excessive load to the cron system
  • Use aggressive JavaScript or caching logic that interferes with WP-Cron triggers

To find the source of the conflict:

  1. Temporarily switch to a default theme such as Twenty Twenty-One.
  2. Use a methodical approach to deactivating plugins:
    • Disable all non-essential plugins.
    • Re-enable your backup/scheduling plugin only.
    • Run the cron job. If it succeeds, the issue is almost certainly one of the disabled plugins.
    • Enable plugins one by one, checking the cron job manually after each activation.

Look especially at these categories:

  • Security plugins with login activity trackers
  • Caching plugins (e.g., WP Rocket, W3 Total Cache)
  • Backup competitors running in parallel
  • SMTP or newsletter plugins with their own cron queues

During this process, keep an eye on your cron events using WP Crontrol. A sudden increase in stuck tasks after enabling a specific plugin usually reveals the source.

Step 4: Resolving the Conflict

Once a conflicting plugin is found, you have several options depending on its role and criticality:

  • Replace it: Swap with a similar tool known to be cron-compatible.
  • Update the plugin: Check if a newer version fixes the issue.
  • Contact the developer: Report the conflict with debug logs if possible.
  • Run system cron instead of WP-Cron: For advanced users, disabling WP-Cron and setting a true server-side cron job guarantees reliability.

Disabling WP-Cron is done by adding the following to your wp-config.php file:

define('DISABLE_WP_CRON', true);

Then, on your server, schedule a cron task (e.g., via cPanel or CLI) to run every 5 minutes:

wget -q -O - https://yoursite.com/wp-cron.php?doing_wp_cron >/dev/null 2>&1

Step 5: Monitor and Test Long-Term Stability

Once the issue is resolved, don’t assume it’s fixed forever. Systematically revisit your cron tasks at least weekly during the month after resolution. Reinstall a monitoring plugin like WP Activity Log or use your backup plugin’s log feature to confirm success over time.

Establishing separate cron logs—either via a log management plugin or your server’s cron log terminal—is a good long-term assurance tactic. You may also want to configure alerts that notify you if scheduled backups are missed more than once.

Conclusion

Scheduled WordPress tasks aren’t a “set it and forget it” luxury—they’re mission-critical, especially for backups and transactional operations. When WP-Cron fails silently due to plugin conflicts, the consequences can be severe. But with a structured approach—starting with identifying the symptoms, resetting the cron system, and isolating plugin incompatibilities—you can restore full automation and regain confidence in site reliability.

Treat your cron system with the same respect you do your admin credentials or payment gateways. After all, in times of crisis, your backups and automations are what bring your digital investment back from the brink.