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 both write to the same SKU, they take turns overwriting each other. One app pushes a quantity, the other pushes a different one, the first resets it on its next run, and so on. Your available quantity flaps back and forth, sometimes several times an hour.
The overlap to worry about is stock, because stock is what this app writes to Amazon. It does not write prices or listing content, so it cannot fight another app over those. What it can do is contradict another app's inventory push, and that is more than enough to hurt you.
The consequences are real. 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. Amazon Seller Sync does not write prices to Amazon at all, so it cannot be one of the two apps fighting here. Tick this if another app is repricing you, so you know where a moving price is coming from.
Inventory and stock sync. Which app pushes your available quantity to Amazon. This is the one that genuinely matters, because Amazon Seller Sync does push merchant-fulfilled stock. 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. Amazon Seller Sync does not write listing content to Amazon, so again it is not a party to this fight. Tick it so the check is accurate.
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. Work out which app made the last write, and re-run the conflict check.
Amazon Seller Sync is easy to rule out here, because it does not write prices or product content to Amazon at all. The only thing it writes to Amazon is merchant-fulfilled stock, through Inventory Sync. If your Amazon prices are moving on their own, something else is moving them.
Also see Troubleshooting and the Setup checklist.