Check for conflicting apps is step 2 of the setup checklist. It exists to stop a specific and expensive failure: two apps writing to the same Amazon listings at the same time.
It takes a couple of minutes and it is worth doing properly, even if you are fairly sure you have no other Amazon app installed.
Amazon does not know or care which app sent an update. It simply applies whatever arrives last.
So if Amazon Seller Sync and another app are both managing the same listing, they take turns overwriting each other. The other app sets a price, the repricer sets a different one, the other app resets it on its next run, and so on. The same happens with stock. Your listing price and your available quantity flap back and forth, sometimes several times an hour.
The consequences are real. You may sell at a price you did not intend. You may oversell stock you do not have, because two apps each think they own the quantity. And repeated contradictory updates make it very hard to work out what actually happened, because the state you see in either app is only whichever write landed most recently.
This is not a problem you can safely leave and sort out later. Decide which app owns each function before you turn anything on.
The check inspects your store for the fingerprints other Amazon apps leave behind, specifically their metafield definitions and their registered fulfilment services. It recognises:
The generic match is deliberately broad, so it can flag an app that is harmless. That is why the check ends with a decision from you rather than an automatic block.
Note
The check reads what is installed on your Shopify store. It cannot see what is configured inside another app, so it cannot tell whether that app is actually pushing to Amazon or merely sitting there. Only you know that, which is why the modal asks.
Everything in the modal is framed around four functions, because these are the four things two apps can fight over.
Pricing / repricing. Which app decides what your Amazon price is. If another app reprices, and you also enable the Amazon Seller Sync repricer, the two will chase each other inside their own separate floor and ceiling rules.
Inventory and stock sync. Which app pushes your available quantity to Amazon. Two sources of truth for stock is the fastest route to overselling.
Creating and editing listings. Which app owns the listing content: title, bullets, images, attributes. If both publish, your listing copy will be overwritten unpredictably, and any AI-written copy you applied here can be replaced by the other app's version on its next push.
Fulfilment (FBA / MCF). Which app routes Shopify orders to Amazon for fulfilment. Two apps sending fulfilment requests for the same order can double-ship it.
You do not have to hand all four to one app. It is perfectly reasonable to let another app keep listings while Amazon Seller Sync does pricing, as long as exactly one app owns each function.
Select Run check on the setup card. If nothing is found, the step is marked done and you can move on.
If something is found, the modal Is another app managing your Amazon? opens.
You can confirm again to override and continue.
This is deliberate. The conflict check is a warning, not a hard block. The app cannot see inside the other app's settings, so it has no way to prove you have switched anything off. There are also legitimate reasons for a detection to persist: the other app may still be installed but idle, its metafield definitions may linger after you disabled its sync, or the generic "amazon" match may have caught an app that does nothing to your listings.
So the final decision is yours. If you know the other app is no longer writing to Amazon, override and carry on. The step is then marked done and the setup checklist moves on.
Warning
Overriding does not resolve the conflict, it only silences the warning. If the other app really is still pushing prices, stock or listings, your Amazon data will keep flapping and the app cannot prevent it. Only override once you are genuinely confident the other app is no longer writing to Amazon.
If prices or stock start changing in ways you did not ask for after setup, come back to this check. The most common cause is an app you forgot about, or one whose sync was re-enabled after an update. Turn the Amazon Seller Sync Repricer off while you investigate, work out which app made the last write, and re-run the conflict check.
Also see Troubleshooting and the Setup checklist.