Shopify store maintenance is easy to skip because Shopify runs the hosting for you. But hosting is only part of the job. Themes fall out of date, apps leave code behind, tracking quietly breaks and former staff keep their logins. I built and maintained Shopify stores for the clients of a UK digital marketing agency for about two years, and in my experience most problems on a live store are small things nobody checked. Here is the monthly checklist I’d give any owner, plus the jobs to do each quarter and each year.
What Shopify handles, and what is still your job
Shopify takes care of hosting, SSL certificates and PCI compliance for card payments. It can also apply automated bug and security fixes to themes from the Theme Store, without changing your design or settings. Everything else is yours: newer versions of your theme, your apps, your product data, your tracking and who can get into your admin.
The monthly Shopify store maintenance checklist
Pick a fixed day each month and work through these in order.
1. Theme updates
Check the Themes page for a new version of your theme. Shopify adds it as a draft theme and copies over your theme editor settings. Code edits are another matter: if they conflict with the update, Shopify shows a message that the code edits could not be included, and you have to carry them across yourself. That’s why heavily customized themes fall behind. Read the release notes, test the draft, then publish. Before any code change, duplicate the theme, because the code editor’s file history restores one file at a time and can’t bring back deleted files.
2. Apps and leftover code
Go through your app list and your bill, and remove what you no longer use. Uninstalling stops future charges, though you may still pay for the current cycle, and it doesn’t cancel charges an app bills outside Shopify. Some apps also leave code in your theme, so search your theme files for the app’s name after each uninstall.
3. Speed
Open the web performance reports under Analytics. They track your store’s Core Web Vitals over time. Google’s “good” thresholds are LCP within 2.5 seconds, INP within 200 milliseconds and CLS of 0.1 or less. If a number slipped, look at what changed that month: a new app, a homepage video or oversized images.
4. Broken links and redirects
Check Google Search Console for new “Not found (404)” pages and redirect each one to the closest live page under Content, Menus, View URL redirects. Shopify only redirects from URLs that are actually broken, so a redirect won’t work while the old page still exists. When you change a product or collection URL handle, make sure the option to create a redirect is selected.
5. Product data
Spend twenty minutes on product hygiene: missing images or alt text, thin descriptions, wrong weights that break shipping rates, missing SKUs, products in the wrong collections, and sold-out products with no plan. Bad data loses sales quietly.
6. Checkout and payments
Place a real order on the live store, ideally with a discount code, then cancel and refund it, and check the confirmation and shipping emails. Shopify also has a test gateway and a Shopify Payments test mode, but customers can’t place live orders while your payments are in test mode, so use those on a development store or in a quiet hour. A real test order may cost a small processing fee. That’s cheaper than a broken checkout.
7. Tracking
Compare last month’s Shopify orders with the purchases recorded in GA4 and your ad platforms. A big gap means something broke, usually after a change to apps, the theme or checkout. Settings, Customer events shows which app pixels and custom pixels are installed. If the numbers don’t match and you can’t see why, my conversion tracking service traces it end to end.
8. Staff, collaborators and two-step authentication
Go to Settings, Users. Remove people who have left and collaborator accounts for developers or agencies whose work is done, and check that everyone has only the permissions they need. Everyone should sign in with two-step authentication or a passkey. Each person sets this up for their own account; on Plus you can require it for everyone. Keep your recovery codes somewhere safe.
Backups: what Shopify does and does not cover
This one catches owners out. For backing up your store, Shopify’s Help Center points you to CSV exports (products, customers, orders, gift card codes, discount codes and financial data), a downloaded copy of your theme, or a backup app from the Shopify App Store, rather than a built-in restore button. It also notes limits, such as orders that can’t be imported back through the admin.
What I recommend:
- A monthly export of products and customers, saved outside Shopify.
- A downloaded copy of your theme before every update or code change.
- A backup app for stores where losing a day of product edits would really hurt.
Quarterly and yearly tasks
Every quarter:
- A full app audit covering cost, overlap and speed impact.
- A walk through the store on your phone, as a customer, from search to order confirmation.
- A review of your Shopify Flow workflows and anything else connected to the store.
- A check of policies, shipping rates and tax settings against how you actually work.
Every year:
- Confirm your domain renews automatically and the card on file is valid. For domains managed by Shopify, renewal is charged about two weeks before the registration ends.
- Review your plan against your sales, staff numbers and card fees.
- Decide whether your theme still fits, or whether a redesign would do more than another round of patches.
- Remove any collaborator account or app you can’t explain.
If your theme carries years of custom code, moving those features into proper theme sections can make every future update easier. That’s the kind of cleanup I take on as part of my Shopify development work.
Quick checklist
- Theme update checked, tested as a draft and published.
- Unused apps removed and leftover code cleaned up.
- Core Web Vitals reviewed for any slip.
- New 404s redirected.
- Product data gaps fixed.
- Live test order placed, refunded and emails checked.
- Orders matched against GA4 and ad platforms.
- Staff and collaborator access reviewed, two-step authentication on.
- Exports and a theme copy saved outside Shopify.
Related reading: Shopify Flow: 10 Automations That Save Store Owners Hours and Shopify Metafields and Metaobjects, Explained for Store Owners.
FAQ
How long does monthly Shopify maintenance take?
For a small store with a stable catalog, this checklist usually fits in an hour or two. Stores with frequent launches, many apps or custom code need more time.
Does Shopify back up my store?
Shopify looks after its own platform, but for your store’s data its Help Center points to CSV exports, theme downloads and backup apps. Don’t assume you can roll back a mistake.
Should I install theme updates as soon as they appear?
Not straight onto the live store. Add the update as a draft, read the release notes, test your key pages and checkout path, then publish. If your theme has custom code, budget time to move those edits across.
Can I hand maintenance to someone else?
Yes. Give them collaborator access with only the permissions they need, agree what they check each month, and ask for a short written report every time.
Not sure what your store has been missing? Get a free website review and I’ll point out the maintenance jobs your store needs first.
