Record Customer Payments and Partial Payments

Last modified: June 9, 2026
Estimated reading time: 5 min

Monitoring Invoice Payment Status for Property Managers

If you own income-producing real estate, you know one of the most tedious tasks is invoicing and making sure your tenants pay their rent each month. And when their lease includes late fees, you need a quick and easy way to see which tenants have paid and which are past due. STRATAFOLIO offers invoicing that syncs with your QuickBooks accounts and provides a payment status snapshot, so you can quickly track paid and overdue invoices.

How Pending Payments Affect Your Invoice Balance

When a tenant submits a payment through the Tenant Portal, it does not always clear immediately. ACH transfers and other electronic payments take time to process, so a payment may remain in Pending status for several business days before it is fully confirmed. To keep your records accurate and to prevent tenants from accidentally paying the same invoice twice, STRATAFOLIO treats a Pending payment as a promise that the funds are on the way.

This means a Pending payment will reduce the outstanding balance on the related invoice while it is still being processed, even though the money has not yet reached your account. The invoice may appear fully paid or partially paid in your dashboard and on the Tenant Portal during this time. Once the payment fully clears, nothing changes on the invoice. If the payment fails, the balance will reopen so the tenant or your team can take action.

This behavior is intentional and protects both you and your tenants. Without it, a tenant could log in to the Tenant Portal, see an outstanding balance while their ACH payment is still being processed, and submit a second payment to cover what appears to be an unpaid invoice. That would result in a duplicate payment, an overpayment, and extra reconciliation work for your team.

Why You Should Add Invoices for Your Tenants

Creating monthly invoices for all your tenants in your QuickBooks is a best practice. This does not mean you have to send the invoices to the tenants, but that they should have an invoice added. This helps with the following:

  • Verifying the correct amount of Rent and NNN Charges are being invoiced to the tenant
  • Make sure that you are not missing any escalations of rent
  • Checking to make sure that the tenant is paying their invoices on time
  • It is better business practice to show a paper trail for all Rent and NNN Charges if ever needed

In STRATAFOLIO, we show all payments collected from the tenants on a cash basis. This is another reason to ensure invoices are added in QuickBooks or STRATAFOLIO each month. We will not display Sales Receipts or A/R reports, so the Ices are the best way to track all payments due to your organization.

Steps to Viewing Payment Status

Add an Invoice

To see payment status in STRATAFOLIO, you must add an invoice in either STRATAFOLIO or your QuickBooks account. When you add an invoice in STRATAFOLIO, the invoice is pushed to your QuickBooks account. You can then print or email the invoices straight from STRATAFOLIO.

If any changes are needed to the invoices after they are finalized and in QuickBooks, you must make those updates in QuickBooks. Once the changes are made, QuickBooks will sync back to STRATAFOLIO with the updates.

No matter how you add the invoice (using either STRATAFOLIO or QuickBooks), the invoice information will sync to STRATAFOLIO and can be viewed on the Rent Collection page.

You can find more information about creating invoices in our Knowledge Base article for How to Add Invoices in STRATAFOLIO.

TIP: Using STRATAFOLIO to add invoices ensures that you will automatically capture any rent escalations or NNN changes that were entered for that lease.

Record Payments in QuickBooks

To have the status of the invoices accurately reflected in STRATAFOLIO, payments received must be properly posted to the correct invoice for the Customer/Tenant in QuickBooks. Once the payment is posted to the invoice in QuickBooks, it will be updated in STRATAFOLIO shortly.

You can find more information about posting payments in our Knowledge Base article How to Receive Payments in STRATAFOLIO.

NOTE: QuickBooks Online will sync with STRATAFOLIO whenever you make a change to your account. QuickBooks Desktop must be synced with the Web Connector to see the updates made in STRATAFOLIO.

REMINDER: STRATAFOLIO is only as up to date as your QuickBooks account!

How to Record Partial Payments in STRATAFOLIO

If you enter a payment amount that is less than the invoice balance, STRATAFOLIO will treat it as a partial payment. The system will apply the amount received to the selected invoice and continue to display the remaining balance as outstanding. This ensures you can track exactly how much is still owed.

Partial payments will sync to QuickBooks along with the invoice details. The unpaid portion will remain open until additional payments are recorded, bringing the invoice balance to zero. Overdue balances will remain marked as past due on the Rent Collection page until the invoice is paid in full.

Navigate to the Rent Collection Page

The quickest and easiest way to view the payment status for multiple invoices is to run a report from the Rent Collection page. Using the left side navigation panel, select Rent Collection under Operations.

Navigate to the Rent Collection Index Page through Operations from the left-side navigation menu

Select Dates & Sort on Balance

Select Dates

  • The Rent Collection page defaults to the next month, on the 16th of the month. You must select the date range and view options you want to use for current/past invoices.
  • Once you have selected the date range, bring the past due balances to the top by selecting Balance.
Utilize the top dropdown filters for the Rent Collection Index Page especially the Date filters to locate invoices faster and sort based on Balance

Scroll right to see more information, or select the green Invoice # block to open the invoice and view the details.

Additional Sort Options

Hierarchy Search in the Rent Collection Page

  • On the Rent Collection page, you can also narrow the search to a specific Organization, Entity, Building, and all the way down to the Tenant level.

Invoiced Search in the Rent Collection Page

  • You can select Not Invoiced, Draft Invoice, Sync Error, Sync in Progress, & Finalized in the Invoiced search block. This is especially helpful if you prepare the invoices ahead of time and want to find all the draft invoices that need to be finalized.

Balance Search in the Rent Collection Page

  • In the Balance search block, you can narrow the search by invoices that are Overdue, Current, or have a Credit.

Export Report

In the Rent Collection, you also have the option to export the report to Excel, PDF, or CSV.

Use the button to export the report into the format you want

For more information about the Rent Collection page, see our Knowledge Base article about the Rent Collection page.

How to Add Invoice Payments

We know owners and managers encounter many different situations, and sometimes, it is easier to post your invoiced rent payments in STRATAFOLIO rather than QuickBooks. Since STRATAFOLIO syncs with your QuickBooks account, adding a payment to one account (either QuickBooks or STRATAFOLIO) will be reflected in the other.

One advantage of adding payments through STRATAFOLIO is that all your QuickBooks accounts are accessible in one place. In STRATAFOLIO, switching between separate QuickBooks accounts to add payments is quick and easy. In fact, in STRATAFOLIO, there is no “switching” because all invoices appear in a single location on the Rent Collection page.

Receiving payments is a simple process within STRATAFOLIO.

Navigate to The Rent Collection Page by Going to the Left-Side Menu, Selecting Operations and then Rent Collection.

  1. The first step is to select the outstanding invoice(s) to which you want to add the payment.
  2. Next, select Add Payments.
Select the checkbox next to the tenant and select the button to Add Payments

Add the Payment Details

  1. Select the Date the payment was received.
  2. Identify the Type of payment received: Cash, Check, ACH, or Other.
  3. Add any Reference to help you track the payment received, such as the check number.
  4. Select the asset account to which the payment will be posted in QuickBooks.
    • In QuickBooks, you typically post a deposit to Undeposited Funds and then move it to another account. You can use STRATAFOLIO to post the payment to any asset fund for QuickBooks.
  5. Select the invoice(s) that were paid and the amount paid. If the amount received differs from the balance, you will need to adjust the Amount Received.
    • All invoices with an outstanding balance for the selected tenant(s) will be displayed.
    • You cannot post an amount greater than the amount due on the invoice. If you need to apply an overpayment to an invoice, do so in QuickBooks.
  6. Select Add Payments. QuickBooks and STRATAFOLIO will sync at the next scheduled QuickBooks Desktop sync, or within minutes for QuickBooks Online.

NOTE: A payment needs to be posted in only one location, either QuickBooks or STRATAFOLIO. If you made payments in QuickBooks, please synchronize, then allow some time for STRATAFOLIO to reflect those payments.

Click On A Tags To View Related Content: Invoicing Leases Property Manager Rent Collection Tenants

Continue reading

Previous: Guide to the Investor Dashboard
Next: How to Input and Manage a Loan in STRATAFOLIO