The 9 Best Payroll Software with Direct Deposit in 2025

ByEric Czerwonka Last Updated
5 Best Payroll Software with Direct Deposit

The best payroll software will make it easy for your team to set up direct deposit and receive their earnings on time and into their bank accounts via secure ACH transfer. 

It will also give your team a self-service employee portal where they can make changes as necessary to their direct deposit info and tax withholdings, see exactly how much money they made, and view the breakdown of their earnings.

Finally, it will streamline your entire payroll process. Payroll software works best when it streamlines everything from time tracking to issuing additional earnings (bonuses, commissions, reimbursements, etc.).

Below, you’ll find the nine best payroll software with not only direct deposit but also other features that small businesses need to make running payroll quick and painless.

1. Buddy Punch

Buddy Punch is a cloud-based time tracking, employee scheduling, and payroll application that lets you manage all of your key administrative tasks in a single tool.

As a time-tracking tool, employees clock in and out using the Buddy Punch app (available for the web, iOS, Android, and ChromeOS). Everyone’s hours are compiled into timesheets, and hours and overtime are automatically calculated for you.

With PTO accruals, you can set Buddy Punch up to manage your paid time-off program. Buddy Punch automatically calculates how much PTO employees have earned. They can request PTO at any time through the Buddy Punch app. And when that PTO is approved, it’s automatically added to timesheets.

You can also create employee schedules in Buddy Punch using its drag-and-drop scheduling tool. This lets you take advantage of features that help you save on labor costs, such as punch limiting and automatic clock-outs.

Punch limiting prevents employees from clocking in before they’re scheduled to work, and automatic clock-outs automatically clock employees out at the end of their shifts. These features help you keep labor costs down and prevent employees from earning unintentional overtime.

Finally, since you already have all of your payroll data in Buddy Punch, paying your employees is quick and easy through Buddy Punch payroll.

How Buddy Punch Payroll works

Buddy Punch payroll’s features include tax filing, direct deposit service, and compliance support, making payroll processing smoother and more efficient.

To set up Buddy Punch payroll, you start by setting up your company in Buddy Punch. You can create workspaces for different locations or for remote employees, and you can set up benefits deductions for things like insurance, HSAs, child support, and retirement contributions.

An address must be entered for each new employee you create. This lets the system know what federal, state, and local taxes need to be withheld from the employee’s paycheck. Tax calculations are computed automatically.

Contractors can also be paid using Buddy Punch. When you create a new employee profile, simply select whether they’re a W-2 employee or a 1099 contractor. This lets Buddy Punch know not to remove taxes or other benefits from contractors’ payments.

Once the company is set up and employee profiles are created, employees can set up their accounts. They can enter their bank details to set up direct deposit of their paychecks, and they can also review their pay stubs in Buddy Punch anytime.

Finally, you can choose two-day or four-day payroll processing. If you choose two-day processing and want your payday to be on a Friday, you will submit your payroll no later than two days prior (i.e. the end of the day on Tuesday).

Running payroll with Buddy Punch

Once you’ve reviewed all employee hours — or a supervisor has approved all of their team members’ timesheets — it’s time to run payroll. Simply click the “Run Payroll” link in the payroll dropdown.

Next, click “Import time into payroll.” This grabs all time clock data from the pay period and adds it to your payroll report.

You’ll be taken to the “Run Payroll” page where you can do a final review of all time data and add custom earning rates or make adjustments if necessary. You can also choose how you want to pay employees — either via direct deposit into employees’ bank accounts or manually by mailing them a paper check.

When all edits are complete, you can preview your payroll to see a quick breakdown of all of your employees’ and contractors’ pay along with your cash requirement — the amount needed to fund payroll. 

Finally, you submit your payroll to start its processing. You’ll be able to see the status of the payroll at any time — whether it’s pending, drafted, or paid — from the Buddy Punch Payroll dashboard. 

You can also download a payroll journal if needed from completed pay periods, track payroll tax deposits on the “Tax Deposits” page, and access/download important filing authorizations (like Form 941) under “Documents.”

Features to keep your payroll accurate

Beyond tracking time and running payroll, Buddy Punch comes with lots of optional features that help you keep your employees honest and your payroll accurate:

  • Geofencing: Use Buddy Punch’s geofencing feature to designate a particular radius, or geofence, around a particular business location or job site. If an employee attempts to punch in outside of the geofence, they will be asked to try again in the right location.
  • IP address locks: If all of your employees work in an office, you can set up IP address locks that prevent your employees from clocking in and out unless they’re connected to your office’s Wi-Fi. This is a great alternative to geofencing for office workers.
  • Photos on Punch: Use Photos on Punch to require a photo from staff whenever they clock in, which includes a clear image of their face and surrounding background. Administrators can easily review these photos within the Buddy Punch dashboard.
  • GPS tracking: For field workers or remote employees, you can capture their locations when they clock in/out to make sure they were on site when they punched. Or you can set up real-time GPS to track workers’ locations throughout the day.
  • Overtime alerts: Get a notification when an employee is nearing overtime so you can adjust their schedule and avoid unplanned overtime costs.

Buddy Punch has many more features in addition to the ones discussed above. You can explore all of them here. 

Customer reviews

At the time of writing, Buddy Punch has an overall rating of 4.8 out of 5 stars across 1,000+ reviews on Capterra. Here’s what one customer has to say about its payroll features:

“Buddy Punch helped our business reduce a lot of costs related to human resources management, payroll, and time tracking. We implemented this software as our employees exceeded eight because we were finding it difficult to keep track of time, work, payroll, etc. This software has really helped us in this regard, and we also saved a lot of time.”

Pricing

Pricing for Buddy Punch’s time-tracking software starts at $4.49 per user per month plus a $19 base fee. The payroll service is an additional $6 per user per month plus a $39 per month base fee.

Want to learn more about Buddy Punch? Start a free trial — no credit card required — take an interactive tour of the product, or request a personalized demo.

2. QuickBooks Payroll

QuickBooks Payroll is a great option for businesses that rely heavily on QuickBooks Online or Desktop for accounting software. Its seamless integration with other Intuit products makes running payroll simple, and if you subscribe to the Premium or Elite package, you also get its time-tracking software for free.

Key QuickBooks Payroll features include:

QuickBooks Payroll has an overall rating of 4.4 out of 5 stars on Capterra across 876 reviews. Here’s what customers like about the platform:

“I found QuickBooks Payroll particularly impressive for its seamless integration with QuickBooks Online for accounting, comprehensive tax compliance features, and user-friendly interface for managing payroll and tax processes efficiently.”

3. Paychex Flex

Paychex Flex is a great direct deposit payroll service for small business owners who are looking for something easy to use and implement. It has an employee self-servicing feature that allows employees to complete some of the administrative work themselves and provides transparency with taxes and their pay. Other key features include:

Paychex has an overall rating of 4.2 out of 5 stars on Capterra across 1,617 reviews. Here’s what customers like about the platform:

“Paychex Flex offers a user-friendly interface that simplifies payroll processing and HR management tasks. The dashboard is intuitive, making it easy to navigate through different features, whether you’re handling payroll, benefits administration, or employee time tracking. The mobile app is also a significant advantage, allowing users to manage tasks on the go.”

4. ADP RUN

ADP RUN is a full-service payroll provider that’s best for bigger businesses, as well as those with other ADP products. It’s catered towards larger companies with features like multi-jurisdictional payroll and multi-company management. ADP RUN is also the only option on this list that offers background checks, even in its essentials package.

Key features include:

ADP RUN has an overall rating of 4.5 out of 5 stars on Capterra across 782 reviews. Here’s what customers like about the platform:

“Run ADP was intuitive and easy to navigate and use, even for a non-HR person. I was able to take care of payroll quickly and efficiently without any of the bugs or quirks that some of the other payroll software programs seem to have. If I had a question or needed help with anything, their customer service was available and incredibly helpful.”

5. Gusto

Gusto is a great option for automated payroll. Many of the other services listed here will have some manner of automation, but Gusto has the most amount of automation in every part of their features. It also has options for multiple pay schedules and off-cycle payroll. Key features include:

Gusto has an overall rating of 4.6 out of 5 stars on Capterra across nearly 4,000 reviews. Here’s what customers like about the platform:

“This system is not only easy to set up but is incredibly user-friendly. The system tracks all of our payroll, PTO, and tax information and all but runs itself. After having used a few other options, this was by far the best value for our money.”

6. Rippling

Rippling is a great option for startups and those looking for customization, as Rippling allows you to do many things such as create unique pay options, run payroll as much as you want, and even create unique policies. Some of Rippling’s most unique features include:

Rippling has an overall rating of 4.9 out of 5 stars on Capterra across 3,095 reviews. Here’s what customers like about the platform:

“My overall experience with Rippling has been positive. The platform’s all-in-one approach to HR and IT management has helped streamline many of my day-to-day tasks. Having access to everything from payroll and benefits to device management within a single interface has made it much easier to manage my work-related needs.”

7. Justworks

Justworks is a great option for businesses with employees across states, as many of its features are specifically catered towards making sure that you’re complying with state and federal laws. Justworks can also be a great option for more irregular-paying jobs, like tip-based or commission work. And in addition to its payroll software, it offers a full suite of HR tools.

Other key features include:

Justworks has an overall rating of 4.6 out of 5 stars on Capterra across 726 reviews. Here’s what customers like about the platform:

“We love the easy functionality of the website. The time tracking and time off features have been great in implementing consistent policies. We employ people in multiple states, so the work they do to manage the unemployment accounts in each state has really been the backbone that has allowed our rapid growth.”

8. OnPay

OnPay is a great option for businesses that also need HR options, as OnPay has many HR options paired with their payroll features. Though many of the other options on this list have HR options, none of them have the same number as OnPay, and the payroll system works well in sync with those HR features.

Key features include:

OnPay has an overall rating of 4.8 out of 5 stars on Capterra across 439 reviews. Here’s what customers like about the platform:

“I have an employee with two local city withholdings and a school district withholding that I thought I was going to have to manually withhold for. Turns out that a few minutes with online chat support is all it took to get OnPay to handle it.”

9. Square Payroll

Square Payroll is best for small businesses, as well as businesses looking for ways to have their employees paid quickly. Square Payroll has many features that allow for different pay options, as well as next-day direct deposit and even same-day deposit for employees that use Cash App. Other key features include:

Square Payroll has an overall rating of 4.7 out of 5 stars on Capterra across 610 reviews. Here’s what customers like about the platform:

“Like many small businesses, payroll is not something I know how to do. I needed a quick and easy way to handle this and still be in compliance with all the laws. It’s a bit daunting, but Square Payroll made it so simple. I don’t have to worry about anything because they handle everything with incredible efficiency.”

Choosing the best payroll software for your business

The best payroll provider for your business will depend on your business size and unique needs:

  • If you want to consolidate multiple processes and tools into one and run payroll easily and affordably, Buddy Punch is a great choice.
  • If QuickBooks Online or Desktop are integral to how your business operates and you don’t mind a higher monthly cost, you’ll probably want to go with QuickBooks Payroll.
  • If you’re looking for something simple for a business with few employees, check out Gusto, Paychex, and Square — which is particularly good for businesses already using Square’s point-of-sale system.
  • ADP RUN is great for large businesses with complex needs.
  • Rippling is great for tech companies with employees working across the globe.
  • Finally, if you need payroll and HR-specific features for things like hiring and onboarding, OnPay and Justworks are great tools to consider.

Whichever option you go with, spend the time needed upfront to make sure it’s right for your organization. 

Switching payroll solutions later can cause a lot of work and headaches — and delay your ability to pay your employees — so make sure you do your due diligence and explore the tools you’re considering fully before making a final choice.