Agree with the others here, this does sound more like a cart/app conflict than a Shopify checkout issue itself.
The key thing I’d test is whether the checkout button is being re-rendered or temporarily hidden when the cart updates. This can happen when a cart drawer, shipping app, upsell app, discount app, or AJAX cart script modifies the cart state after page load.
A few practical checks I’d run:
-
Test the full journey on both desktop and mobile
Product page → add to cart → cart page/cart drawer → checkout -
Temporarily disable cart-related apps one by one
Especially anything touching shipping, upsells, discounts, cart validation, or the checkout button. -
Check the browser console when the button disappears
If there is a JavaScript error during the cart update, that will usually point you in the right direction. -
Compare behaviour in a duplicated theme
If the issue disappears in a clean theme or with apps disabled, you can narrow it down much faster. -
Be careful with CSS-only fixes
Forcing the button to stay visible can hide the symptom, but if the underlying cart state or checkout payload is broken, customers may still hit problems later in the journey.
The important thing is to test the full path to purchase, not just whether the button appears. A store can look fine visually but still have a broken buying journey after an app or theme change.
For transparency, I build Revenue Shield, a Shopify app that continuously tests these buying journeys across desktop and mobile and alerts you if cart or checkout flows break. Not needed to debug the root cause here, but this is exactly the kind of issue automated journey testing is designed to catch before customers do.