MembershipWorks works well with QuickBooks Desktop and QuickBooks Online, however Quickbooks Online does have some advantages:

• With QuickBooks Desktop, it is important to be careful not import the same transaction twice; this will create duplicate transactions. There is no way for QuickBooks Desktop to determine if the transaction has previously been imported. So if you export by dates from the Dashboard > Financial, once you have imported transactions for a certain date, make sure you do not overlap that date in the future. 
• For QuickBooks Desktop, exports should only be done after all transactions are finalized. For example, there is no way to update transactions such as a subsequent refund in Quickbooks Desktop. However with Quickbooks Online, MembershipWorks can update these types of transactions with changes that occur later.