9 Best Direct Deposit Payroll Software for Small Businesses

If you’re tired of cutting paper checks and are ready to migrate to a payroll system that lets you pay employees via direct deposit, one of these nine payroll software with direct deposit — each designed specifically for small businesses — will help you make the shift.

Features to look for in direct deposit payroll software

In terms of payroll processing, there are four key features you’ll want to make sure your software has:

• The ability to calculate, file, and pay federal, state, and local taxes.
• The ability to handle your specific pay schedule (weekly, bi-weekly, monthly, etc.)
• The ability to calculate overtime and include overtime/bonus pay in paychecks.
• The ability to remove garnishments and voluntary deductions from paychecks.

In addition to these basic features, you’ll also want to look for features that make paying your employees via direct deposit easier:

• Same-day or next-day deposits help avoid delays in employees receiving their pay.
• Employee self-service options let employees enter/update their bank information, view their paystubs, and change their withholdings on their own.
• Integrations with the other systems you use, such as accounting software and time tracking apps, makes running payroll quicker, easier, and less error-prone.

However, instead of relying on integrations, you may want to look for software that offers other HR features — like time tracking, scheduling, employee onboarding, benefits administration, and performance reviews — in addition to payroll processing and direct deposit. 

Finally, you’ll want to find an option that’s easy to use with a simple, intuitive interface and offers great customer support. Payroll is critical for proper accounting and employee engagement, so you’ll want to be confident that the provider you choose will be there to support you when you run into issues.

The 9 best payroll software with direct deposit

Below, you’ll find our reviews of what we determined were the best payroll software with direct deposit after testing dozens of options. For each option, we dig deep into features, pricing, and customer reviews to help you find the perfect software for your small business.

1. Buddy Punch

Best for small businesses seeking a time-tracking integration with their payroll software.

Buddy Punch is a combined 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. And since you already have all of your time-tracking 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 deposits, 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.

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 employees paid on a Friday, then 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 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 dashboard. 

You can also download a payroll journal if needed from completed pay periods, track 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

Buddy Punch’s payroll features are only available as an add-on to its time tracking software. Its time tracking packages start at $4.49 per user per month plus a $19 per month base fee that covers all admin users. The payroll add-on costs an additional $6 per user per month plus a $39 per month base fee. 

All together, you’ll pay a base $58/month fee plus an additional $10.49 per month for each employee you add to the system. For the cost, you’ll get access to time tracking, PTO tracking, GPS tracking, payroll processing, direct deposit, tax filings, and expert payroll support. 

2. QuickBooks Payroll

Best for small to medium-sized businesses already using QuickBooks for accounting.

If your organization uses QuickBooks Online heavily for accounting, QuickBooks Payroll can be a good option. Since both tools are made by Intuit, the process of integrating the data between the two systems is seamless. This eliminates the need for double data entry and ensures your financial data is accurate and up-to-date.

Key features

• Same-day and next-day direct deposit options
• Automatic tax calculations, filing, and payments
• Tax penalty protection guarantee covering up to $25,000
• Employees can access their pay stubs, tax forms, and benefits information

Customer reviews

QuickBooks Payroll has an overall rating of 4.4 out of 5 stars on Capterra across more than 900 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.”

Pricing

QuickBooks Payroll offers a discount to new users for the first three months: you’ll pay a base monthly fee of $42.50 per month plus $6 per employee per month. After the discount period, the base per-month fee jumps to $85 per month plus $6/user/month.

It’s worth noting that all QuickBooks products are sold separately, so if you want to use QuickBooks Online for accounting, QuickBooks Payroll for payroll, and QuickBooks Time for time tracking, you’ll have to pay separate subscription fees for each product.

3. Paychex Flex

Best for growing businesses with diverse payroll needs.

If your business is growing and you’re struggling to navigate new compliance issues, Paychex Flex is a good option to consider. Paychex Flex assigns a dedicated payroll specialist to every one of its customers, so in addition to direct deposit payroll software, you’ll get access to an expert who can provide guidance and support.

Key features

• Pay employees via direct deposit (same day), paper checks, or pay cards
• Optional add-ons ensure you’re only paying for the features you need
• HR features like benefits management, time tracking, and recruiting
• Tools for handling employee classifications
• Affordable Care Act (ACA) reporting

Customer reviews

Paychex Flex has an overall rating of 4.2 out of 5 stars on Capterra across more than 1,600 reviews. Here’s what customers like about the platform:

“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.”

Pricing

Pricing for Paychex Flex is not publicly available. You can contact their sales team to get a quote. 

4. ADP RUN

Best for international payroll support.

ADP RUN is a great option for small businesses that currently have international employees and that plan to grow in the future. It offers international payroll through its integration with ADP Global Payroll, and its features can scale as your workforce expands through ADP’s other extensive HR and benefits solutions.

Key features

• Pay employees via direct deposit, paper checks, or pay cards
• Pay international team members in compliance with local labor laws and tax regulations
• Multi-jurisdictional and multi-company management
• HR features like employee background checks and unemployment management
• Reports for monitoring payroll, expenses, and tax data across regions

Customer reviews

ADP RUN has an overall rating of 4.5 out of 5 stars on Capterra across 780+ 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.”

Pricing

Pricing for ADP RUN is not publicly available. You can request a quote through their website. 

5. Gusto

Best for small to medium-sized businesses looking for an all-in-one payroll and HR platform.

Gusto is a payroll and HR solution that’s particularly well-suited for small to medium-sized businesses that value ease of use, affordability, and robust employee management features. It provides comprehensive payroll and HR features, including direct deposit, tax filing, and benefits management — all in a single platform.

Key features

• Integrated time-tracking tools and time-off management features
• Manage health insurance, retirement plans, commuter benefits, and more
• Employees can access pay stubs, W-2s, benefits information, and time-off requests
• Automates payroll tax calculations, filings, and payments at the local, state, and federal levels and across multiple states
• New hire onboarding features like offer letters, digital document signing, and automated forms for tax and benefits enrollment

Customer reviews

Gusto has an overall rating of 4.6 out of 5 stars on Capterra across more than 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.”

Pricing

Gusto’s Simple plan starts at $6 per person per month plus a $40 per month base fee and includes single-state payroll, basic hiring and onboarding tools, and Gusto-brokered health insurance administration. To add time tracking to this plan, it’s an additional $6 per month per person, and next-day direct deposit is an additional $15/month plus $3/person/month.

Gusto’s Plus plan eliminates the need for the time tracking and next-day direct deposit add-ons, including those in the cost of the plan. After an initial 3-month discount period ($60/month + $9/person/month), you’ll pay an $80 per month flat rate plus $12/person/month. This gets you access to multi-state payroll, next-day direct deposit, and time tracking.

6. Rippling

Best for businesses that want to integrate payroll, HR, IT, and benefits management.

Rippling is ideal for businesses that need an all-in-one solution for payroll, HR, and IT. It’s particularly well-suited for tech-savvy companies, startups, and those with remote or international teams. If you value automation, scalability, and the ability to manage diverse administrative tasks in one platform, Rippling is an excellent choice.

Key features

• Pay employees via direct deposit, paper checks, or paycards
• Issue and manage employee devices, software access, and security settings
• Automated set up of payroll, benefits, and company devices for new hires
• Keeps up with tax and labor law changes automatically
• Handles compliance with local tax and labor laws in over 50 countries

Customer reviews

Rippling has an overall rating of 4.9 out of 5 stars on Capterra across more than 3,500 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.”

Pricing

Pricing for Rippling is not publicly available. You can request a quote through their website. 

7. Justworks

Best for businesses needing Professional Employer Organization (PEO) services.

Justworks is an excellent choice for businesses seeking Professional Employer Organization services. As a PEO, Justworks becomes a co-employer, sharing legal responsibility for employees. It also negotiates with providers to offer your team access to premium insurance plans, often at rates that are typically only available to large corporations.

Key features

• Get access to Fortune 500-level benefits, including insurance and retirement plans
• Handles compliance with labor laws, employee classifications, and tax regulations
• Administers multi-state payroll and handles compliance
• Employees can manage their benefits, access pay stubs, and review tax forms
• Employee onboarding features like digital offer letters, e-signatures, and automated setup for payroll and benefits

Customer reviews

Justworks has an overall rating of 4.6 out of 5 stars on Capterra across 700+ 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.”

Pricing

Justworks has a non-PEO payroll-only plan that starts at $8 per person per month plus a $50 per month base fee. This plan only includes payroll, time tracking, and HR features — not any of the PEO benefits.

The PEO plans range from $59/person/month to $599/person/month. On the $59 plan, Justworks shares legal responsibility for your team but doesn’t negotiate benefits for you. For benefits negotiation, you’ll need to be on the $109/person/month PEO Plus plan. Global teams will need to be on the $599/person/month EOR plan.

8. OnPay

Best for small businesses with straightforward payroll needs.

OnPay is ideal for small businesses that want an affordable, reliable, and easy-to-use payroll solution. It’s perfect if you’re looking for a reasonably priced tool that handles payroll, taxes, and basic HR needs without unnecessary complexity. While it lacks many of the features of other tools on this list, that can be ideal if you’re looking for something simple.

Key features

• Multi-state payroll with tax calculations, filings, and payments for federal, state, and local 
• Pay employees via direct deposit, paper checks, or paycards
• Employee self-service for viewing pay stubs, accessing tax forms, updating personal details, and managing direct deposit preferences
• HR features like hiring and onboarding, benefits administration, 401k, and Workers’ Comp

Customer reviews

OnPay has an overall rating of 4.8 out of 5 stars on Capterra across 400+ 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.”

Pricing

The great thing about OnPay’s pricing is that it only has one plan that includes all of its features, so you don’t have to scroll through complex feature comparison tables to determine what you’ll need to pay. Its plan is $6 per person per month plus a $40/month base fee.

9. Square Payroll

Best for small retail or service businesses that are already using Square for payments.

Square Payroll is ideal for retail, restaurants, and service businesses that already use Square’s payment processing system. It makes it easy to automatically sync sales data, track employee hours, and run payroll without the need for manual entry.

Key features

• Track employee time using your existing point-of-sale (POS) system
• Multi-state payroll with automated tax calculations and filings for federal, state, and local taxes
• Pay employees via check, direct deposit, or Cash App
• Employees can access their pay stubs and tax forms and update their personal information
• Manage benefits like insurance, PTO, and 401k plans through the platform

Customer reviews

Square Payroll has an overall rating of 4.7 out of 5 stars on Capterra across more than 600 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.”

Pricing

Square Payroll is one of the lowest-cost apps on this list, with pricing starting at $6 per person per month plus a $35 per month base fee. All features are included on that plan.

If you don’t have employees and just need to pay contractors, you can use Square Payroll for those payments for just $6/contractor/month — no base fee is charged for contractor-only payments.

Choosing the best payroll software for your team

The best payroll software for your business will depend on your unique needs: 

• If you want to consolidate time tracking and payroll into one easy-to-use and affordable platform, Buddy Punch is a great choice.
• If QuickBooks Online is integral to how your business operates, you’ll probably want to go with QuickBooks Payroll.
• If you’re looking for something with basic, affordable features, check out Gusto, OnPay, and Square Payroll.
• ADP RUN and Rippling are great options to consider for businesses with more complex payroll and compliance considerations.
• Justworks and Paychex Flex are worth considering if you want to take a more hands-off approach to payroll and benefits administration.

Whichever option you go with, spend the time needed upfront to make sure it’s right for your organization. Switching payroll providers later can cause a lot of rework 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 choice.