MarginEdge & Quickbooks Desktop | Integration FAQs

How does this work? 

  1. What does MarginEdge send to QuickBooks? 

MarginEdge sends invoices and journal entries (sales data, inventory adjustments and non-AP expenses). Invoices, sent as bills, show up in Accounts Payable (AP). These bills can be paid in QuickBooks.  

  1. How does data flow from MarginEdge to QuickBooks? 

Data flows easily between the two systems. When you want your invoices, sales entries, and inventory adjustments from MarginEdge to be imported into Quickbooks, you’ll run Quickbooks Web Connector from Quickbooks Desktop which will sync the two systems. This option is within Quickbooks.

In “manual mode”, you’ll select what information gets queued to MarginEdge each time you sync the systems, or you can choose “auto-mode” where the information will queue up automatically. See question 8 and 9 for more details on these options.

Wait, you’re not going to mess with my QuickBooks, are you?  

  1. Will I have control over the content and the timing of what comes into QuickBooks? 

Yes, you’ll have several different ways to modify and control how MarginEdge sends your data.  


  • Invoices – at onboarding, you can determine how  invoices are coded; from then on, you can control:
    • Category totals (MarginEdge and accounting categories)
    • Dates (payment dates, due dates, etc.)
    • Vendors (with a suite of options for how each vendor  is processed)  
  • Sales entries – you can control: 
    • What categories they are associated with
    • What lines are included
    • How they look (sales entries are identical to before) 


  • By default, nothing is sent to your accounting system without your authorization (manual mode) 
  • Invoices are processed 24-48 hours after MarginEdge receives them; they are then available for approval to  flow into your accounting system.  
  • For your convenience, invoices can flow automatically into QuickBooks without any layers of approval (auto-mode).  
  1. Does MarginEdge edit/update/manipulate my vendors or chart of accounts? 

No! We never edit or update your chart of accounts in QuickBooks in any way.  

  1. Can you split a product into different accounting categories? 

Yes. You can split products into accounting categories by percentage (e.g. 30% of lemons go to the bar and 70% go to the kitchen).  [Learn more in this article on Product Categories

  1. Does MarginEdge change transactions after posting in QuickBooks? 

No! Once we send an invoice, payment, or sales entry to QuickBooks, we never adjust it. If you need to make a change, you can delete it in QuickBooks, and then resend the data from MarginEdge; but we never alter data in your accounting system.  

If you use Bill Pay, when a bill is paid we will mark it as paid in accounting (but the bill data will not change in any way). See question 15 and 16 for more information on Bill Pay.  

  1. Does MarginEdge control payment terms for my vendors? 

No. The source of payment terms is the accounting system. When MarginEdge sends bills to QuickBooks, the due dates are based on the vendor terms you set up in QuickBooks.  

  1. Can I have complete control over what gets sent to my accounting system? 

Yes. For invoices, inventories and sales, there are options to be in “manual mode.” This means that you must manually select every invoice, sales entry and inventory adjustment to be queued to go into accounting. The alternative is to be in “auto-mode.” We find most clients who start in manual mode quickly switch to auto-mode once they are comfortable with the platform.  [Learn more in this article about export settings]

  1. What gets sent to accounting automatically in auto-mode? 

Regardless of the setting, the user always has to run Quickbooks Web Connector to pull information from our system. As invoices, sales entries, or inventory adjustments are processed and ready to be imported into Quickbooks, they are automatically flagged in MarginEdge as “Pending.” You can pull the information right from Quickbooks; you don’t need to go into MarginEdge.  

In auto-mode (used by 90%+ of our clients), every invoice, sales entry, and inventory adjustment that is closed is immediately queued to accounting. The accountant does not have to select individual invoices, sales entries, or inventory adjustments to be queued to accounting.  

  1. If I’m in auto-mode, how will I use MarginEdge? 

In general, for invoice and sales data, you won’t need to go into MarginEdge. However, for some tasks, you’ll need to use MarginEdge to: 

  • Research invoices, quickly get invoice info by vendor or by period for easy vendor statement reconciliation 
  • Investigate an invoice missing from the accounting  system 
  • Change the category for a product 
  • Change a setting for a vendor  

Invoice Processing  

  1. Can I flag invoices for review? 

Absolutely. We have settings for requiring a second layer of review. You can choose this option for all invoices, invoices above a certain dollar amount or for any accounting category.  [Learn more in this article on Setting up Invoice Approval

  1. What if a really old invoice comes in? Will I know if that happens? 

If you’ve closed the books for the period that the invoice is dated in, we will code the invoice to the current period. If you have not closed the books for the period, the invoice will be coded in that period. 

We have a Close Book feature that lets you lock the books a set number of hours after the period ends. This ensures MarginEdge stays in sync with QuickBooks and past financial reports.  

  1. What happens if I’ve already paid an invoice by check or ACH? 

If an invoice is uploaded that has a payment indicated (e.g., a handwritten check number or ACH debit is noted), we will send both the invoice AND the payment info over to accounting. 

  1. What happens if I’ve already paid an invoice by credit card? 

For invoices paid by credit card, MarginEdge sends these expenses not as a bill and as AP, but as a journal entry, booking the amount to an expense (e.g., $100 to Food), and booking the amount also to the credit card account you specified.  

Paying Bills 

  1. Could I pay bills right from the MarginEdge platform? 

Yes! With our Bill Pay feature, you can select invoices and schedule them to be paid.  

  1. How will QuickBooks know I’ve paid these invoices? 

Payments are synced to QuickBooks as checks marking the invoices as paid, making bank reconciliation easy. 

Sales data 

  1. Can MarginEdge use classes for sales and invoice data?  

Yes and yes.  

  1. What do sales from MarginEdge look like in QuickBooks? 

Journal entries. MarginEdge exports sales information (including payment methods, comps, discounts, etc.) from the client’s POS system early each morning following the  close of business. Sales can be customized to fit your needs and appear how you’ve always formatted the data.  

  1. Can MarginEdge send sales entries as sales receipts rather than as journal entries? 

No, we only support journal entries.  


  1. Are there charges / limits to support?

No, support is no charge and unlimited.

Further Reading


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