How to Back Up WooCommerce Stores Step by Step

Your WooCommerce checkout broke after a routine plugin update. You restore yesterday’s backup. 23 orders vanish. Those customers are calling. That’s the nightmare – data rollback solving one issue while quietly nuking your latest sales.

Backups are all about having the right kind, rather than just having one.

WooCommerce is actually alive with orders, customer data, inventory changes, and simple backup methods miss that.

Let’s go over how to back up your store without losing a single order, even during a disaster. From real-time syncing to transaction-safe snapshots, you’ll learn how pros protect revenue, not just files.

Why WooCommerce stores need different backup rules than regular WordPress sites

Most WordPress sites can survive a bad backup strategy. Lose a blog post? Annoying, sure – but you rewrite it, move on. WooCommerce is different. Lose orders, and you’re explaining to angry customers, reconciling stock, maybe even missing payroll. That’s a whole different level of risk.

WooCommerce needs a smarter backup strategy because it runs on live, transactional data. Every order is trust and logistics in motion.

Here are four common failure modes – and how each can wipe out critical order data:

• Botched updates can break your checkout process, causing orders to be interrupted and if a restore is rolled-out, you may lose records of previous orders. This means revenue is lost, and customers are left frustrated, unable to complete purchases.
• Security breaches often corrupt your store’s data, forcing a restore from backup. Unfortunately, that process can result in lost orders, leaving you with missing sales and damaged trust.
• Human error happens when settings are changed or and it seriously impacts the system. A restore from a backup might fix the issue, but it may erase recent transactions, further disrupting operations.
• Host failures like server crashes or corrupted disks can lock you out of your site. Without a recent backup, you risk losing all order data and wasting time trying to rebuild from scratch.

The hidden cost of daily backups: How many orders can you afford to lose?

When you opt for daily backups, you’re accepting up to 24 hours of potential data loss. If your store processes 100 orders a day, this could mean 100 lost transactions in the event of a failure.

This cost isn’t just about the lost revenue; you also need to factor in the damage to customer trust and operational setbacks. Daily backups might sound safe, but they don’t account for real-time threats like server crashes, hacking attempts, or database corruption.

For serious WooCommerce stores, regular automated backups give you the best chance at recovery. In any worst-case scenario, you minimize the amount of recent sales data and customer information at risk.  

Many overlook the maintenance mode workflow – a key part of order preservation during backups. While performing a backup, switching your site to maintenance mode can help eliminate data integrity issues during major operations by temporarily preventing new orders.

However, this approach isn’t practical for most active WooCommerce stores that serve customers around the clock – putting a live store into maintenance mode means downtime and potential lost sales.

For that reason, maintenance mode is best reserved for scheduled maintenance windows or low-traffic periods. In most cases, automated real-time or incremental backups are the safer, more practical way to protect orders without disrupting sales.

Hourly backups may not be enough for your store’s security, but while real-time backups offer the best protection against data loss, they can also increase resource usage and costs.

What happens to today’s orders when you restore yesterday’s backup (and how to save them)

Restoring yesterday’s backup to recover from issues using simplistic backup mechanisms will overwrite your store’s data, including today’s orders. This means all orders placed after the backup was created could be lost.

When you perform a restore, the database reverts to the exact state it was in at the time of the backup, and any new data – including orders, customer information, or product updates – will be replaced by older versions.

To prevent losing orders, follow these steps:

• Back up today’s orders first to avoid losing any new data. Ensure you have the data of current order backed up, and so that you have some reference information, you could also export the current orders using a tool like WooCommerce Order Export (bearing in mind exports don’t represent a complete backup of WooCommerce orders).
• Test restores on staging to catch potential issues before they affect your live store. Running restores in a controlled environment lets you spot failures like long outages or stalls at critical points.
• Use incremental backups to backup more quickly and reduce the gap between restore points so that you can recover more data completely.

When every backup plugin times out: Real solutions for large WooCommerce stores

When dealing with large WooCommerce stores, it’s common to encounter PHP memory exhaustion errors, particularly with larger sites with many plugins running. An error like this can appear as:

Fatal error: Allowed memory size of 536870912 bytes exhausted (tried to allocate 12345678 bytes) in /wp-includes/class-wp-db.php on line 123

This means your store’s memory limit is too low to process such a large database during a backup.

Here are a couple of things you can do to address this issue:

• Increase memory so you have enough to back up large stores without running into timeouts. You can do this by editing your wp-config.php file or adjusting the PHP memory limit directly in your hosting control panel. Since optimal limits vary by host, it’s best to consult your hosting provider to determine safe and supported memory settings for large backups.
• Use command-line alternatives to bypass PHP’s limitations if your backups service supports WP-CLI. This way, you can run backups directly from the server’s command line, which doesn’t rely on the browser’s memory limits. This method is often faster and more reliable for large databases.
• Understand host process limits to avoid hitting server restrictions. Some hosting environments set hard limits on PHP processes or max execution times. Contact your host to increase these limits, or consider switching to a more scalable solution like VPS or dedicated hosting.

ShieldBACKUPS uses its own secure internal storage system, bypassing local server bottlenecks entirely by handling backups off-site through its managed infrastructure.

This is especially beneficial for stores that have outgrown other backup methods, as it eliminates issues like timeouts, storage limits, and slow performance. With four daily backups, you get comprehensive protection throughout the day.

Plugin vs cloud vs manual: Which WooCommerce backup method works best?

When choosing a backup method for WooCommerce, you should prioritise one that handles order preservation well – particularly during mid-day order spikes, true disaster recovery, and crisis practicality.

Method	Order preservation (mid-day orders)	True disaster recovery	Crisis practicality
Plugins	May miss orders during high-traffic hours; intervals can lead to gaps.	Slow restore process, prone to failure under load.	Requires manual intervention, can lead to timeouts and memory issues.
Cloud	Better at real-time order preservation but still dependent on server speed.	Faster restores, but may experience delays during high traffic.	Reliable for disaster recovery, but integration must be flawless.
Manual	Complete control, but manual effort means orders may be missed during active times.	High control, but requires immediate action – no automation.	Impractical for large stores due to the need for constant monitoring.

ShieldPRO combines security and backups, offering a streamlined solution that combines backup with security measures, ensuring both your store’s data and its protection are handled simultaneously.

Backing up directly to S3 natively prevents local storage bottlenecks, while the security features safeguard against vulnerabilities.

For agencies, the unlimited-site license adds even more value, allowing backup and security for all clients under one account.

This two-for-one approach makes ShieldPRO the ideal solution for stores that need both reliability and comprehensive security.

The security hole nobody mentions: Your backup credentials are a ticking time bomb

Storing backup credentials – whether for Dropbox, S3, or other services – directly in your WordPress configuration poses a security risk.

If a hacker breaches your WooCommerce store, they also gain immediate access to your backup credentials, putting your data at risk. Once the attacker compromises these credentials, they can manipulate, delete, or steal both your live site and your backups, leaving you vulnerable to complete data loss.

Our 3-2-1 backup strategy can help you really secure your data through redundancy and separation:

• 3 copies of data, meaning your live site plus two separate backups, to ensure full redundancy and protection.
• 2 different media formats storing your backups. For example, one copy could be kept on a local server for quick access, while another could be stored in cloud storage like S3 for added security.
• 1 secure off-site location to store an archive. Using cloud storage ensures that your backup remains safe, even if your primary site is compromised.

These are, of course, the minimums. Feel free to add redundancies to your heart’s content as long as you’re also taking the right precautions to secure those backups.

Alternatively, you could use ShieldBACKUPS. Its zero-credential architecture and managed storage eliminate the vulnerability created by storing backup credentials within WordPress. This way, a breach of your site won’t give an attacker access to your backup data.

Instead, we use secure, managed AWS storage for direct-to-S3 backups, ensuring your backups are stored safely in a highly secure, off-site location – completely separate from your site’s environment.

How to manually back up WooCommerce

When you need to back up your WooCommerce store manually – for updates or troubleshooting – you have more control over everything. While the process is time-consuming and prone to error, it’s a reliable fallback.

Here’s how to manually back up your WooCommerce store:

1. Connect to your website using either an SFTP client or your hosting control panel’s file manager.
2. Download the wp-content folder, which includes your plugins, themes, and uploads – where WooCommerce settings and media files are stored.
3. Access phpMyAdmin through your hosting control panel.
4. Select your WordPress database from the left-hand menu.
5. Choose the Export option and select the Quick export method in SQL format.
6. Download the database file to your local system.

Back up your WooCommerce store with ShieldPRO today!

Don’t wait for disaster to strike your WooCommerce store. Every day without proper backups is a gamble with your business, your customers’ trust, and your revenue.

ShieldPRO’s ShieldBACKUPS delivers four daily automated backups with direct-to-S3 streaming, bypassing the storage bottlenecks and timeout issues that plague other solutions. No more worrying about lost orders, corrupted data, or security breaches wiping out your hard work.

With zero-credential architecture and managed storage, your backups stay secure even if your site gets compromised. Plus, you get comprehensive security protection bundled with your backup solution – two critical needs solved with one powerful tool.

Stop risking your store’s future. Protect every order, every customer, and every dollar with ShieldPRO’s reliable backup and security solution today.