Direct Deposit: Getting Started Guide

Q. Why should I set-up direct deposit?

A. Direct deposit is convenient if you want to run payroll on autopay. This makes sense if your employee’s hours are always the same each week. If your employee’s hours vary, you can manually create the pay stub each week and select direct deposit as the method of payment. Direct deposit will be an additional payment method and will not remove the other ways to pay you have been using.

Q. How do I enroll into direct deposit?

A. You must be subscribed to either the Essentials Plus or Professional plan, only available through our website. To upgrade your subscription, if needed, login at this link: https://app.nestpayroll.com/login using the same email address and password you use to login to the app. Then, send us a text or email to request direct deposit (650-460-1750 or support@nestpayroll.com). Within two to three days, you’ll see an action item on your main dashboard to secure your account. If you need to pay your employee in the meantime, continue using the method of payment you have been using before direct deposit.

Two simple steps to set up direct deposit: 

  1. Complete Secure your account.  If you still have the message on the app’s main dashboard Secure your account, you will need to complete that before direct deposit is an option. This includes micro-deposit verifications to your bank account which may take 2-3 days.

  2. Once secured, tap on Enable Direct Deposit on the main dashboard to invite your employee to self-enroll. After you send the invite, your employee will receive an email with a link to a secure web page for bank account set-up. The link expires after six hours. If your employee needs a new link, tap on “Enable Direct Deposit” again.


    After your employee has finished entering their bank account, you can start paying with direct deposit. There are 2 ways to use the Direct Deposit Payment option:

  • Manually each time: After approving a pay stub, select the Bank Transfer/Direct Deposit option from the list of payment methods. 

  • Automatically each week: set the payroll to run automatically as a Recurring paystub (cancel any previous recurring) with Direct Deposit. This will remove the requirement to approve and pay each pay stub manually each week. Easily set this up when you go to create a pay stub. 

Important to know:

  • Direct deposit takes four to six business days (weekends and holidays do not count) for the money to arrive in your employee’s bank account after the pay stub is paid, standard with the ACH (Automated Clearing House) system.

  • If your employee needs the funds more quickly, you can approve the pay stub to pay in advance before the work period is over. If you schedule the pay stub to be recurring on autopay, you can set the pay date to be earlier in the week.

  • Employees do not use the app. They will receive an invitation via email with a secure web link for them to enter their bank information via the web.

Q. How do I run payroll?

A. Click on your employee's initials on the main dashboard. Enter the hours (pay periods are weekly) and any overtime hours. Click Continue and review the summary. If it looks correct and doesn’t need editing, click Approve. Once you approve it a screen will come up to select how you want to pay the “on the books” amount. You can also set up recurring/direct deposit (autopay) when creating a pay stub (see instructions below).

Once the paystub status changes from Pending to Processing, the Void option will be grayed out and you will not be able to cancel the pay stub or the payment.

Q. Can I still use the other ways to pay my employee?

A. Yes, you can choose what works best for you and your employee each week:

  • bank transfer/direct deposit (four to six business days for net pay to be received by employee)

  • integrated mobile payments (Square’s Cash App or Venmo)

  • pay separately through your own favorite payment app or write your own check

Q. How do my employees add their bank accounts to receive funds?

A. This is easy if you have completed securing your account.

  1. Secure your account first. If you still see the message on the main dashboard to “Secure Your Account”, please finish that process first.

  2. Click on Manage (to the right of the Your Team section), click on your employee’s name, tap “Invite to setup bank account”. 

    Your employee will receive an email invitation to enter their bank account. For security reasons, the link will work for only six hours. If your employee misses the six hour window, resend the invitation.

  3. Once your employee has added their bank account, you will see “Bank Account on file” in your employee’s profile. 

  4. The next time you approve a pay stub, you can select Bank Transfer as the payment method and your employee will receive funds within 4-6 business days. 

    Note: Employees do not use the app. They will receive the invitation via email with a secure link for them to enter their bank information.

Q. How do I set-up direct deposit on autopay?

A. Once the employee has added their bank account, you can pay them with direct deposit (bank transfer on autopay).

  1. Tap on your employee’s initials to create a new pay stub.

  2. At the top, select Make recurring paycheck (tap to become green).

  3. Auto-Pay with Direct Deposit will appear when you select the recurring paycheck option. This option is appropriate if your employee’s hours worked are the same every week, and you are comfortable with the funds automatically being deposited to your employee each week without your intervention. You can turn this feature off at any time, but keep in mind that you can’t cancel a transaction if it’s already been initiated.

  4. It takes 4-6 business days for the employee to receive funds. If you want your employee to receive funds sooner, and the amount you pay doesn’t vary each week, select a day before the work week is over to initiate payment, as shown below.

Direct deposit on autopay: Day of week for pay stub approval matters.

A recurring pay stub + Direct Deposit, as shown in the screenshot here with the two green buttons turned on, makes the most sense if your employee’s hours are the same each week. If so, you can set the pay stub to be approved before the work week is over so your employee receives the net pay faster.

For example, if your employee’s last day of the work week is a Friday, you could select Tuesday to initiate payment. It takes 4-6 business days, so your employee will receive payment typically the following Monday after the pay period, instead of a full week later.

This only makes sense if you pay the same each week. If hours vary, it’s better to approve a paystub each time manually for accuracy, so don’t turn on both green buttons. You can still make it recurring, which will allow you to edit the pay stub each time it’s created. You will still need to manually approve it.

Q. I want to pay every two weeks but only see weekly as the option.

A. Nest Payroll uses weekly pay periods because government agencies require hourly/non-exempt wages to be evidenced in weekly periods due to overtime laws, and some states mandate weekly payroll for household employees (NY for example). If you prefer to pay every two weeks, here are two convenient solutions:

  1. set up direct deposit with autopay so you can set it and forget it (pay stubs remains weekly) OR

  2. pay two pay stubs at the same time every two weeks (the pay stubs remain as weekly).

If you choose to pay manually (not autopay), make the pay stub recurring so you won't need to remember or double check which weeks you paid. The pay stubs will be waiting for review on the main dashboard. Every two weeks you simply approve the two paystubs waiting on your dashboard, and you can always edit the hours or the other items if you need to before approving each one.

Q. Oops, I approved a pay stub and I realize it’s wrong. Can I delete it and create a new one?

A. It depends on the timing.

If you paid with bank transfer/direct deposit, go to Recent History, tap on the paystub and see if VOID is available. If available, tap on VOID which will cancel the paystub and the transaction. The deadline for voiding an Auto-Pay recurring paycheck is 3:59pm Eastern Time on its scheduled pay date which initiates the process. Once VOID is unavailable, you cannot cancel the transaction.