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We are trying to find a Quickbooks API to integrate our custom app with Quickbooks Desktop and Quickbooks Online without having to write to them both separately. It seems like the best approach is to write to the Quickbooks Online Services, where the desktop data is sync'd using Quickbooks Sync Manager, and hopefully allows us to also access customers using QBO.

Is there something that will sync to both QBD and QBO?

Our app is written in .NET using C#

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We are trying to find a Quickbooks API to integrate our custom app with Quickbooks Desktop and Quickbooks Online without having to write to them both separately.

There isn't one.

where the desktop data is sync'd using Quickbooks Sync Manager,

Sync Manager is deprecated - relevant blog post.

Is there something that will sync to both QBD and QBO

No.

Realistically, the data models between QBO and QBD are very similar. You still have customers, and invoices, and invoice lines, and items, and etc. So, you're not looking at 100% code duplication here - just the data format/protocol you're actually submitting stuff to QuickBooks with is different.

So you're probably looking at upwards of 60%+ code re-use even though you have to use two different APIs.