I receive the money on invoice to clear it out as payment, puts it in my Profit. also when the money is deposited and i reconcile it also putting the money to my profit

Then you are doing something wrong. Deposits are NOT income, only cash flow. Payments should post to Undeposited Funds. Then create a deposit that includes all funds from UF in that deposit.

Single payment deposits can be posted directly to banking. My guess is you have a bunch of payments sitting in Undeposited Funds and are mistakenly ADDING bank feed deposits as income.

The above mistake is about the only way you can double up income

I am following in the footsteps of someone else and have discovered that there is over $300,000 in my undeposited funds account.  It goes back to July of 2017, when the business opened.  Can you please tell me how I can clean this up?

Hey there, Sophie25.

You can clean it by depositing it to the right bank account. Here's how:

1. Click the Plus sign (+) icon.
2. Choose Bank Deposit.
3. Choose the payments you will deposit.
4. Click the Account drop-down arrow, then choose the correct bank.
5. Click Save and close.

As always, I suggest conferring with your accountant on the best way to handle this since they're past transactions. This might affect the reconciled months.

If you have other questions or concerns, don't hesitate to reach out again. I'll be here anytime.

I tried doing what you said but it changed my bank balance.  I know that my bank balance is not off by more than $300,000.   Currently what the bank says and what QBO says is only off by around $400.  I've worked with QuickBooks Desktop before but never Online.  I'm finding the transition rather difficult.  Can you please tell me what I am missing in trying to figure this out?  

I think I might have figured at least some of it out.  Please let me know if I am close.  On a daily basis, I export invoices and payments from our software to QBO.  There is never a balance due as all invoices are paid at the time of service.  Instead of exporting both invoices and payments, should I only be exporting the invoices and then applying them to the payments as they are deposited into the bank.  The majority of payments are made with a debit or credit card.  Cash and checks make up the remainder.  I don't know if this is anywhere close to being right. 

I'm having a hard time understanding why I can't figure this out and get my head around all of this.  I worked with the desktop version for several years and never had this much trouble figuring out where things go.  I guess having the bank activity put in automatically is messing with my brain.  Anyway, thanks for all of you help, now and possibly in the future.

Hi there, @sophie25.

Allow me to join this thread and share some more information about linking your deposits with invoices.

If you've added the deposit transaction through online banking in QBO, you're doing the right thing in only importing your invoices. Next step you need to follow is to link the deposit to an invoice:

1. Click Accounting.
2. Select Chart of Accounts under the Toolbar.
3. Find the account you deposited the payment to, then select View Register (or Account History).
4. Locate and choose the correct deposit.
5. Select Edit.
6. On Bank Deposit screen, scroll down to Add funds to this deposit, then find the fund you need to edit.
7. Choose the appropriate Customer name.
8. In the Account column, search and select Account's Receivable.
9. Select Save.

For more insights, please refer to this article: How to link a deposit to an invoice. That should keep you going today, sophie25.

Please know that I'm still here to offer help if you have additional questions or concern. Just leave a comment below or mention my name. Wishing you and your business continued success!

I did what you said @HoneyLynn_G.  I was able to put the fees with the invoice to correctly account for the deposit amount but it added the invoice to accounts receivable.  If I have received the funds and properly put them to the correct invoice, why does it add to a/r?  The amount currently sits in unapplied cash payment income.  (I undid the link.  I was afraid I had messed it up)

Hello there, sophie25.

Let me bring clarifications to your concern about handling deposits and invoices in QuickBooks Online (QBO).

If you're done importing your invoices, the first thing you need to do is to make payment using the Receive Payment. This is for the deposit amount to be added to the correct account before making Bank Deposit.

Here's how:

1. Go to the Plus Sign Menu.
2. Under Customers choose Receive Payment.
3. Select the customer who paid you in the choose a customer field.
4. Enter the necessary information.
5. Click Save and Close.

Once done you can follow the steps provided by my colleague @HoneyLynnG on how to link the deposit entry to your invoice.

In case you need assistance in doing this, feel free to reach out to our Care Support Team.  Here's how to get their contact information: 

1. Go to https://help.quickbooks.intuit.com/en_US/contact
2. Select  QuickBooks Online.
3. Select a category under “What can we help you with?”.
4. Scroll down the page, then click the Get Phone Number.

I'm always around here in the Community anytime you need help with something. Feel free to leave a reply below.

I'm doing what everyone here has said and it is becoming much easier and making more sense but I discovered today that my A/R is showing 3 transactions.  The invoice coming in, the payment going out, and the deposit going out.  Can someone please tell  me what I am doing wrong?

@Charies_M, @HoneyLynn_G

Thanks for sharing a screenshot of your report, sophie25.

I'll join the thread to help you figure out why there are three transactions in the Account Quickreport.

It looks like the payment and deposit are duplicate transactions. An invoice should only have a payment or a deposit. You'll want to delete duplicate transactions to correct this.

To do so, click the deposit transaction, select More at the bottom and choose Delete (see the screenshot below).

You can also check with your third-party software since they can help you map the invoices and payments during the import process. This way, we can avoid the duplicate transactions.

Let me know how this turns out. I'm happy to help some more if you have questions in QuickBooks Online. Have a great week ahead.

Just when I think I have something figured out, it all falls apart again.  Previous answers to my questions have said that I need to receive payments and then link the deposits to the invoices.  I am so confused.  I'm not the original start of this thread. I added to it because it seemed to deal with my issue.  But I think that all of the responses since I joined the thread pertain to my question.  I invoice and receive payment thru another program. Only one customer is invoiced without immediate payment. I no longer import the payment, only the invoices.  I still need to fix things that were messed up in the past by the previous person but am concentrating right now on getting things correct to move forward.  Maybe if someone could read thru the thread, as it pertains to my issue, I could get a clear, concise and complete answer.  

Hello there, sophie25.

I appreciate you coming back. Allow me to better discuss this with you as I want to make sure everything is clear up.

Reading through this thread, I figured out what happened. From your previous post, I believe you're already able to put the fees with the invoice to the correct account for deposit by following my colleague's advice.

With that, what we'll need to do is just receive the payment for both Invoice and Deposit. This will off set the amounts in your Accounts Receivable and will remove the unapplied cash payment income from your Profit and Loss report.

Let's open the payment and select both Invoice and Deposit. I've attached a screenshot below so you'll have better view.

Please don't hesitate to get back to me if you have other questions or clarifications about this. I'm always here to keep helping.

@Charies_M I have done what you suggested for two different customers and it didn't change my A/R at all. I still have 2 negative and 1 positive for each customer affected. 

It changed the open invoices report for each customer from a deposit to a payment, both with negative amounts. ( or vice versa. I've went back and forth so many times trying to see if I did something wrong that I'm not sure now which one it started with. )  

Hi, sophie25.

Thanks for the prompt response. Let's get this straightened out for you.

When recording the payments through deposit the affecting account must be Accounts Receivable (AR). This is to credit the customer balance which you can choose to apply to the open invoices or you can opt to set your QuickBooks to auto apply the credits.

Once the deposit and invoice is linked through Receive Payment, this should zero out the balance on your Accounts Receivable report. In your case, since there is still a negative amount showing on your Open Invoice report, there is a possibility that the amount from the Amount receive field was not zeroed out when you Receive Payment.

To correct this, let's open the payment and change the Amount receive to zero (0) then click Save and Close. I've attached a screenshot for your reference.

That should keep you on the right track. I'm still here if you have additional questions. You have a great day ahead.

Happily that worked beautifully.  And now, to get this straight, in the future I should link the deposit to the invoice and not receive payment?  Am I on the right track with that?  

Hello there, @sophie25.

Thanks for getting back to us and sharing the result of the awesome solution provided by my colleagues. I’m glad to know they were able to help you get back on track.

I'd love to join the discussion and share some further insight on this matter. Moving forward, you'll need to link the deposit to the imported invoice by receiving payment. Select both the invoice and deposit when you process the payment and make sure the amount received is zero to clear your Accounts Receivable. 

That should take care of it. 

Feel free to drop a comment below if you have any other questions about recording payments. I'll be happy to help you out. Wishing you and your business continued success.

Let me see if I have this straight.  I am supposed to split the bank deposit according to the invoices involved and subtract the fees, then receive the payment to both the invoice and the deposit with a zero payment amount?  

Greetings, sophie25.

I'd love to join this discussion and help you get to the bottom of this to avoid any further confusions.

I went through the thread and reviewed everything to make sure that we're on the same page. So far, It's good to see that my colleagues were able to provide you with the right solution in taking care of this.

That said, I'm happy to say that you've got it right. Moving forward, since you already have deposit transactions in QuickBooks, you'll want to split them accordingly to the invoices involved and subtract the fees.

To do so, you'll need to take note and follow what Charies_M suggested. Your deposits should affect the Accounts Receivable (A/R) account. Otherwise, you won't be able to link them to your invoices. I'm also including our detailed guide on how to link a deposit to an invoice that you may find helpful.

As always, should you need further assistance, you can get in touch with our Customer Care Team. They can do screen sharing in a secure environment and walk you through the step-by-step process. Here's how you can reach out to them:

Contact QuickBooks Support

1. Click the link to head to the Official Intuit Contact page.
2. Select QuickBooks Online.
3. Choose Running your business in QuickBooks, then Customers.
4. In section 2, Here's how to connect with a QuickBooks expert, click Get Phone Number.

Please let me know if there's anything else you need, I want to make sure you're taken care of. Have a great day!

Thanks to everyone who responded and helped with this issue.  I believe that it is solved and I am on the way to getting everything sorted out.