Accounts Integration

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I am currently doing all my financial accounting through Wave but feel this is a very crude system.  It doesn't take into account selling fees deducted by PayPal, Shopify and other platforms that I use.  Is there an all in one accounts system that slots in with Shopify and takes all these fees into account.  I use QuickBooks for my other business which is great but I am creating the invoices on that one and they are being paid through PayPal.  With my online shop it is very different.





Shopify Partner
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Hi Hannah,
I represent an app development company and we have 2 listed apps on Shopify for accounting integration for Quick Books and Xero.

Our app for both Xero And QuickBooks is widely accepted.

If you are based in USA, QuickBooks is the best accounting software.

It connects very well with PayPal and most bank feeds. Our bank is very capable of syncing all orders and also all Shopify fees. Happy to answer any specific questions.
The URL to our app is

Thank you,

I'd suggest AccountingSuite for eCommerce integration.


you could use Webgility, but its rather expensive. I do this process myself for all my ecommerce bookkeeping clients to keep their bookkeeping fees to a minimum.


Hi there,

I am a Wave, Xero, and QBO advisor. Out of those three, my personal preference is with Xero, especially when it comes to e-commerce or complex businesses with lots of apps and connections. Wave, as you said, really is very limited app. It is usually good for those who just start to save on costs but still keep at least some kind of financial records. As you grow, you better switch to QBO or Xero. Both Xero & QBO have various integration apps to connect with Shopify. However, in my experience, not a single app (Shopify, CRM, Booking, any type of app) integrates smoothly. You still need to do some manual work in order to keep your books clean. I personally, actually, prefer not to connect most of the apps and, instead, make necessary entries manually. This way you will ensure that information is not lost or recorded properly. If you can't do it yourself, you better ask for help (at least at the beginning). An accountant (or a bookkeeper) could help you out with the workflow and after that you will be able to record everything properly. 

Hope this helps,


Accounting professional with experience in e-commerce and other industries. Specializing in Xero & QBO setups, year-end/period-end catching up, and monthly support
1 Like
Keep in mind, no app will give you landed cost by sku. I create this kind
of detail for each of my eCommerce clients as I balance their Shopify,
Amazon accounts in their chosen accounting software.
New Member
1 0 0

Hi Kumar. 

I am wanting find out if Quickbooks is capable of tracking individual products and separating them out. I have a few products that I need to track and pay out percentage of profits to vendors. Taking into account the processing fees of each transaction as well. Paypal doesn't separate out the transactions by product and they suggested that I do this manually, but as you can imagine that is very time consuming and inefficient. 

Thank you in advance for your assistance.



Quickbooks desktop can handle this, Quickbooks online not so much. I'd check into Sage or AccountingSuite for your needs.