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Getting Started with QuickBooks Payments

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Thanks for choosing QuickBooks Payments to manage your business! We put together a few steps to help you get started, send your first invoice, and get paid faster.


Integrated invoicing and cash flow management are just a couple ways you can accept payments from your customers. Let's get started.



Please note, QuickBooks customers must apply for QuickBooks Payments and be approved before they can begin to use the service.  For more information, review the Intuit Merchant Agreement, privacy policy, and pricing documents here.



Setting up for success

First things first: To take automated payments and send electronic invoices, set up your payments information. We put together a list of a few things you will need to get set up.


Company Settings

Create and Send an Invoice

Choose where to record payments and processing fees for QuickBooks Payments


Company settings


First, start by signing into your QuickBooks account. Select the Settings (Gear) icon.

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Select Account and Settings from the pop-up menu.




Next, review your company info for accuracy. This is what your customers will see on any invoices, credit card charges, or emails sent through QuickBooks Payments on your company’s behalf. Select the Payments tab located on the left side menu and fill out the following information:



  • Business type
  • Contact email
  • Legal business name
  • Federal Tax ID (EIN)
  • Website
  • Address
  • Phone
  • Industry categories
  • Select how much you think you will process monthly using payments.



  • Name
  • Address
  • Phone
  • Date of birth
  • Mobile phone number
  • Last 4 digits of Social Security number



  • Routing number
  • Account number

Once you have completed the forms, select Accept and Submit.  


Note: if you have not set up Payments yet, simply click on the Learn More button and the Finish Setup button on the next screen.


Create and send an invoice


Once Payments is set up and your account is approved, you will be ready to process and send your first invoice. Begin by selecting the (+) plus sign from the top menu, then select Invoice.


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Fill out your customer’s information or choose it from the drop down, if you’ve already entered their information.  When you’re creating your invoice, be sure to select the types of payments you’ll accept.


Then select Save and Send to email the invoice to your customer.

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Congratulations! You have just sent your first trackable invoice with a Pay now button so your customers can pay you securely online through card or bank transfer. You’ll be able to see when your invoice is sent, viewed, and paid through QuickBooks Payments.


Once your invoice has been paid, money will be in your bank account in 2-3 business days for credit and debit cards and up to 5-7 business days for bank transfers.



Note: Stay tuned for more options with QuickBooks Payments to help you get paid faster!


Choose where to record payments and processing fees for QuickBooks Payments


QuickBooks Payments automatically records your deposits, so it is important to make sure that your payments and processing fees will be recorded to the correct accounts.


  1. Select the Settings icon, then Account and Settings.gswp step 1.jpg

     gswp step 8.png

  1. Select Payments from the left menu.
  2. In the Chart of Accounts section, select the pencil (edit) icon.
  3. For Where do you want to record payments? Choose the correct bank account.
  4. For Where do you want to record processing fees? Choose the proper expense account for tracking processing fees.
  5. Select Save.

What’s Next?

16 Comments 16
Level 2

Getting Started with QuickBooks Payments

Thank you for this discussion.   I however, need some more information and maybe you can help.  


Once QuickBooks Payments automatically created a bank deposit and a bank receipt the funds are showing deposited in the checking account of the client.  However, they are still showing in undeposited funds.  Why?


Getting Started with QuickBooks Payments

Hi jsanterre50,


Once you're able to set up the correct account for your payments, all deposits will go directly to the bank register. 


I just need to ask a question for clarification. When you say "they are still showing in undeposited funds," are you referring to payments that are manually received (payments that aren't paid through the Pay Now option) in your QuickBooks? 


Thanks in advance! 

Level 2

Getting Started with QuickBooks Payments

Hello!  Thanks for getting back to me. 


No, when we enter payments thru other ways correctly we get rid of undeposited funds.  It's only when we use Quickbooks Payments do the payments by CC or ACH go to undeposited funds first, than the bank receipt and deposit (that are done automatically because in the invoices we see "deposit") are sent to the correct bank account.  However, we still see the amount in the undeposited funds account.  I know the "How to receive a payment" workflow.  However, Quickbooks Payments does this automatically so why is this still in undeposited funds?

Level 2

Getting Started with QuickBooks Payments

No, only when they hit the "Pay now" button on invoices.   After the funds are automatically deposited in the back after hitting "Pay now" why are they still in undeposited funds?  Since Quickbooks Payments made the bank receipt and bank deposit why didn't they take it out of Undeposited funds?

QuickBooks Team

Getting Started with QuickBooks Payments

Hi there, @jsanterre50.


Thanks for getting back to us. I'm here to help and provide some additional information about QuickBooks Payments. 


QuickBooks Online (QBO) Payments defaulted to Undeposited Funds account. You'll need to deposit the payments to the correct account by processing Bank Deposit to ensure the money you received from payments is accurately recorded.


You can check this article for the detailed steps on how to record Bank Deposits in QuickBooks Online


If the same thing happens, it would be best to contact our Merchant Service Team. They have additional tools to pull up your account in a secure environment and investigate this further. 


You can contact them through this link:


Please let me know how it goes. I'm always here to help if you have any other concerns. Have a good one.

Level 1

Getting Started with QuickBooks Payments

I'd like to know why you don't let people know they will be charge astronomical fees for using credit card payments. I let a client pay with credit card for the last 6 months and only after digging through my bank account realized I was being charged. You should let your clients know they are being charged a fee at the time of the transaction. It's this is a great example of dark UX, it's unethical squeezing extra money out of your users like this. Very disappointed.

Level 1

Getting Started with QuickBooks Payments

Hi J,
I am a longtime user of QB and although I do not use it to the extent I could and should, I just do not have the time to do much but create invoices and process payments. A couple of years ago, we decided at the beginning of the year to start accepting card payments, as more than one client had requested this option. We have a specialty in Political Media Planning & Buying and consequently, some of the political payments were extremely high. I just did not have the time to go back and double check everything for a couple of months prior to the Primary that year and could not believe how much I lost by going this route! The % varied by card, but it is embarrassing to go back to a client and tell them that we now need to charge them for the card transaction fees. One of them wanted to stay on the card method, so I had to go through the extra step to figure out what percentage to add on, so that it would net to the exact amount of the invoice, once fees were taken out. You can't just tack on the regular percentage, because it made the total invoice even higher, taking out even more in fees, so it was THIS amount that had to be figured out or lose more money again. Plus, the convenience was far outweighed by the additional charges. After about six months, we just stopped card payments altogether. We have also been asked about PayPal (more fees) or any method of payment that didn't add exhorbitant fees. I just checked out Venmo, and so far, I don't see any fees added, and it connects directly to your bank account, via the card or to the bank account, which takes a bit longer to post. All in all, good ole checks work the best, although not good for quick turnaround. A number of our political accounts also did direct deposits at one of the branches near them, as they were up and down the state of California, and this bank was large with a branch in just about every town, and that worked great, but more work on the client end. Sorry. Wish I had better news and wish you luck. Everyone wants a piece of your financial pie!

Level 1

Getting Started with QuickBooks Payments

I am a little confused. Are there fees that are on top of the fees listed when you sign up to use this service? Above, J asked why users are not informed that there will be fees charged to users. I just signed up for this service but I did see that there are fees, just like any other service, so I anticipated being charged the percentages listed when I signed up. As a customer, there are several places that I have shopped that tell me there is a % charged for card processing. I figured that as a business owner, since this is not an uncommon practice for businesses to pass that fee along to the clients, it would not be unheard of to do the same if I so decided. 

So.. In reading your conversation, I have to ask, did you miss that part of the disclaimer that there were fees or are you saying there are fees on top of fees that are not disclosed?

I am sincerely asking. 

Level 2

Getting Started with QuickBooks Payments

Hi. Where did you see the fees stated? I have also not seen them. I find this information helpful and do wish that the fees were more prominent. I would like to know what I am getting into before accepting credit cards as forms of payment.

QuickBooks Team

Getting Started with QuickBooks Payments

Hi ncampbell. 


I'm more than happy to elaborate on the credit card fees for you. There are no monthly or setup fees, a 1% fee on bank transfers (ACH) with a maximum of $10. There's a 2.4% fee for swiped credit cards, a 2.9% fee for invoiced and 3.4% for keyed plus .25 per transaction. I'll include a link to our credit card processing service page with this information and much more. 


Credit Card Processing Services


If there's anything else I can help you with, feel free to post down below. 

Level 1

Getting Started with QuickBooks Payments

Is there a setting during the invoicing process, to add the processing fee to the customer credit card transaction? 

For example, I send an invoice to my customer, that will allow a credit card payment. Is there a setting to notify the customer, that the processing fee of $ will be added to the transaction. Click here to accept... Something of that nature???


Getting Started with QuickBooks Payments

Hello there, millsairconditioning.


The option to add a notification abut the processing fee isn't available. If your customer agrees that they will be the one to handle the processing fee, you can add the fee as a second line item on the invoice.


Before doing so, you'll have to add a service item for the processing fee. Let me guide you with these steps:


  1. From the Sales tab, select Products and Services.
  2. Click New and then select Service.
  3. You can enter Processing Fee as the item Name.
  4. Select an Income account.
  5. Click Save and close.


Afterward, you're good to add it to the second line of your invoice. Just a heads up, you'll have to manually calculate the total amount of the processing fee.


I've also added these references when managing payments: 



I'll be around if you still need help. Keep safe!

Level 1

Getting Started with QuickBooks Payments

When will it be an option to send sn invoice through a cell number instead of only email?

QuickBooks Team

Getting Started with QuickBooks Payments

Thank you for joining us here in the Community, @audreyb1.


The ability to send an invoice from QuickBooks Online via text message isn't available. We don't have a specific time frame as to when this feature is going to be available.


However, to make this possible, you can check out for a third-party application that supports this functionality. You may visit our Apps Marketplace to look for an app that integrates with QuickBooks.


Know that our developers are always finding considering new functionalities to be added to cope with your business needs. That said, I'd encourage you to visit our QuickBooks Online Blog site regularly to be updated with our latest news and product road-maps. 


You can always get back to me if you have any other concerns. I'll be around to assist you. Have a good one!

Level 1

Getting Started with QuickBooks Payments

What's unclear is whether payments done with ACH through an Invoice incur the ACH 1% ($10 max) or the Invoiced 2.9% (+$0.25) fee? This is extremely unclear and could be misleading. 

QuickBooks Team

Getting Started with QuickBooks Payments

Let me share some information to clear out the confusion, @nfuller.


When using QuickBooks payments, your customers can pay you using a different methods. The 1% ( $10 max) fee is for ACH bank transfer while the 2.9% + $ 0.25 is when your customer pays using Credit Card - online invoice. 

Just a heads-up, the fees are subject to change. You can visit the QuickBooks Payments website for the most up-to-date info. Also, you can read through this article for more detailed information: What are the fees for QuickBooks Payments?


Leave a comment below if you have other questions or concerns. The Community and I are always here to help.

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