Payroll Software for Accountants

Payroll software can be complicated and confusing for many accountants, but it doesn’t have to be. The fact is, payroll software has come a long way. It’s more user-friendly than ever before. And most importantly, it has features that will help your firm grow.

Here are the most frequentlty used payroll systems.

actiTIME

If you need a high-quality piece of payroll software, you’re probably looking for something that can make your life easier and save you a ton of time. While actiTIME may not be a payroll app as such, it can help you collect pre-accounting data and eliminate any risk of error when doing so.

With this tool, you or your team members can accurately record work hours, run detailed reports, manage projects and monitor task progress. It allows for uncomplicated access to all essential accounting data, including labor costs, and streamlines such procedures as invoicing and payroll.

Time tracking became a breeze

With actiTIME’s mobile app, tracking time on the client’s side became a breeze. Now accountants simply switch on the timer on their phone as they start another task and get accurate time logs without taking notes.Try actiTIME

QuickBooks Payroll for Accountants: Best Overall Payroll Software for Accountants

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Overall Score: 4.69 OUT OF 5

What We Like

  • Unlimited pay runs
  • Fast direct deposits with next- and same-day options
  • Robust tax penalty protection
  • Discounted payroll plans for clients plus free payroll software access for accounting firms (requires signing up for its free QuickBooks Online Accountant tool)

  • Must use QuickBooks for accounting
  • Basic HR features only
  • Tax penalty protection is available only in the Elite plan

QuickBooks Payroll for Accountants Pricing

  • Software fees: Three plans (Core, Premium, and Elite) with monthly base fees of $45–$125 plus $4–$10 per employee, per month
  • Accountant perks: Free access to QuickBooks Payroll Elite if you get QuickBooks Online Accountant; its ProAdvisor discount program deducts 30% from the monthly software base fees and 15% from the per-employee fees—but your firm will be billed
  • Client discounts: Its Direct Discount option offers 30% off the monthly software base fees and 15% off the per-employee fees for your clients’ first 12 months of service—but your clients will be billed

Read QuickBooks Payroll ReviewVisit QuickBooks Payroll for Accountants

If you use QuickBooks for your clients, then we highly recommend QuickBooks Payroll for Accountants. It lets you set client permissions, guarantees tax accuracy, and includes 24/7 support—plus, its accounting and payroll modules sync seamlessly with each other. And, if you sign up for its free QuickBooks Online Accountant solution, you can easily access your clients’ QuickBooks accounts to check their books, edit transactions, and address issues. It even comes with free access to QuickBooks Payroll Elite (which you can use to pay your employees), discount pricing for your clients, and a partner ProAdvisor program with preferential rates for both you and your customers.

Scoring 4.69 out of 5 in our evaluation, QuickBooks Payroll for Accountants earned high marks (4 and above) in nearly all of our criteria given its solid accounting and payroll tools, ease of use, robust reporting, and transparent pricing. Users also appreciate its efficient payroll tools as it helps simplify employee pay processing. However, its limited HR tools prevented it from getting a perfect rating because, unlike ADP and Paychex, QuickBooks doesn’t have a suite of HR solutions for managing the entire employee lifecycle.

QuickBooks Payroll for Accountants Pricing

With QuickBooks Payroll for Accountants, your clients can choose from three QuickBooks Payroll plans (Core, Premium, and Elite) with monthly fees that start at $45 plus $4 per employee. The differences between these plans include access to time tracking, workers’ comp administration, one-on-one HR support, and a tax penalty guarantee. For your new clients, discounts are available but only for the first three months.

Accountants who are part of QuickBooks’ ProAdvisor program can also choose to pay the monthly fees on behalf of their clients. This allows them to enjoy an ongoing ProAdvisor discount. They can also pass the discount to new clients through a Direct Discount option, but this is only for the first 12 months, plus QuickBooks will send the billings directly to the clients.

QuickBooks Payroll PlansRegular PricingClient Discount*ProAdvisor Discount for AccountantsDirect Discount for Clients
Core$45 per month + $4 per employee monthly$22.50 per month + $4 per employee monthly$31.50 per month + $3.40 per employee$31.50 per month + $3.40 per employee monthly
Premium$75 per month + $8 per employee monthly$37.50 per month + $8 per employee monthly$52.50 per month + $6.80 per employee monthly$52.50 per month + $6.80 per employee monthly
Elite$125 per month + $8 per employee monthly$62.50 per month + $8 per employee monthly$87.50 per month + $8.50 per employee monthly$87.50 per month + $8.50 per employee monthly

*Your new clients get 50% off the software base fee for the first three months. Note that the discounted rates may change, so check QuickBooks Payroll’s website from time to time to view the latest promotions on offer.

QuickBooks Payroll for Accountants Features

  • Payroll: Setting up QuickBooks Payroll is very easy, and you can pay contractors, hourly workers, and salaried employees with just a few clicks. It comes with automatic and unlimited pay runs, and salary payouts can be done through paychecks and via next-day and same-day direct deposits. Its mobile app (for iOS and Android devices)—which is our top-recommended payroll app for small businesses—lets you process payroll and even e-file taxes while on the go. While the other providers on this list (except Gusto, Rippling, OnPay, and Patriot Payroll) have mobile apps, it doesn’t offer electronic tax filings.
  • Tax filing services: Apart from year-end tax report prep and delivery, federal and state tax filings are included in QuickBooks Payroll’s tax services. However, if you require local tax filings, you need to get either its Premium or Elite tier. Elite subscribers also get a tax penalty guarantee where QuickBooks will cover all penalties (up to $25,000 per year) in case of tax filing errors—regardless of who made a mistake. The other payroll software for accountants in this guide may offer a similar coverage but only for tax filing mistakes that their representatives will make.
  • Accountant-specific tools: Access to client management solutions and the free QuickBooks Online Accountant tool, including the seamless integration between QuickBooks products, make managing both client payroll and bookkeeping easy for accountants. Its partner program that includes ProAdvisor and client discounts also offers resources to help improve your skills and grow your accounting business.
  • HR features: Employee onboarding, paid-time-off (PTO) monitoring, and time tracking with QuickBooks Time (formerly TSheets) are just some of the HR features that QuickBooks Payroll offers. While it provides an HR adviser and HR support center via its third-party partner (Mineral) to help keep you compliant, these services are unavailable to accountants who are calling on behalf of their clients.
  • Employee benefits: In addition to pay-as-you-go workers’ compensation (via AP Intego), you are granted access to 401(k) plans and health insurance that is available in all US states. This is unlike Gusto’s health benefits that only cover 39 states.

QuickBooks Payroll for Accountants Drawbacks

  • Local tax filings included in higher tiers: You have to convince your clients to sign up for at least a Premium plan if they want full payroll tax filing services (federal, state, and local). While you get preferential pricing under the ProAdvisor program, QuickBooks Payroll for Accountants’ discounted Premium plan ($52.50 per month plus $6.80 per employee monthly) is still pricier than Patriot Payroll—which offers full-service payroll and automated tax filings for only $30 per month plus $4 per employee monthly.
  • Basic HR features: QuickBooks Payroll is ideal for small businesses that only need simple HR tools. If your clients’ HR needs begin to grow and they require additional solutions like hiring and learning management, QuickBooks won’t be a good fit. You may want to consider ADP, Paychex, and Rippling since all three offer a wide range of HR solutions. And while these providers might not have an in-house accounting system as QuickBooks does, their platforms can integrate with several third-party accounting software.

Visit QuickBooks Payroll for Accountants

BEST FOR SERVICE-BASED BUSINESSESFreshBooks


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The most crucial accounting need for most service-based businesses is invoicing. FreshBooks offers more customizations for invoicing compared to other accounting software. Its primary function is to send, receive, print, and pay invoices, but it can also take care of a business’ basic bookkeeping needs as well. This accounting software makes it easier for service-based businesses to send proposals and invoices, request deposits, collect client retainers, track time on projects, and receive payments.Pros

  • Cloud-based
  • User-friendly interface
  • Third-party app integration
  • Affordable
  • Advanced invoicing features

Cons

  • No inventory management
  • No payroll service
  • Mobile app has limitations

Founded in 2003 in Toronto, FreshBooks started as just an invoicing software. Over time, more features have been added and FreshBooks now has over 500 employees.2 There are four different plans, and businesses can get a 10% discount if they choose to pay yearly, rather than monthly. Additionally, FreshBooks offers a 60% off discount per month for six months. The four plans are: Lite at $6 per month, Plus at $10 per month, Premium at $20 per month, and Select, which is a custom service with custom pricing.

The main difference between the four plans is the number of different clients that are allowed to be billed per month. In the Lite plan, up to five clients can be billed per month. In the Plus plan, up to 50 clients can be billed per month. In the Premium plan, unlimited clients can be billed per month. The Select plan also does not have a limitation on the number of clients that can be billed per month, but adds unique features. It costs an additional $10 per month for multiple team members to use the accounting software and it costs an additional $20 per month for the advanced payment feature, which allows users to charge a credit card in real-time or set up a recurring credit card charge for a client.

There are many third-party app integrations available, such as Shopify, Gusto, Stripe, G Suite, and more. A unique feature of FreshBooks is that invoices can be highly stylized and customized for a professional look and feel. FreshBooks is a great tool for budgeting out projects, sending estimates or proposals, and collecting customer payments.

BEST FOR PART-TIME FREELANCERSQuickBooks Self-Employed


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QuickBooks Self-Employed accounting software is our top choice for part-time freelancers and independent contractors who primarily want to track their income and expenses for their tax return. This software is designed for business owners who file a Schedule C on their individual tax return. 

Without keeping up with business activity using a software like this, freelancers would need to dig through all of their bank and credit card statements to add up their income and expenses at the end of each year, which can be quite daunting. QuickBooks Self-Employed will total up all business transactions automatically.Pros

  • Cloud-based
  • Mobile app
  • Track mileage
  • Differentiate between business and personal expenses
  • Syncs with TurboTax

Cons

  • Data cannot be easily transferred to other accounting software
  • Limited reporting
  • Limited invoicing functionality and customization

QuickBooks Self-Employed is an Intuit product with a cloud-based online interface and a mobile app. This software was created to help freelancers stay organized each year for tax season. Features of QuickBooks Self-Employed include tracking mileage, sorting expenses, organizing receipts, sending invoices, and estimating and filing taxes seamlessly through TurboTax.

Users can choose between three plan options: Self-Employed at $15 per month, Self-Employed Tax Bundle at $25 per month, and Self-Employed Live Tax Bundle at $35 per month. There is a 50% discount for the first three months. The two tax bundles include a TurboTax subscription for income tax filing. The Self-Employed Live Tax Bundle also gives you access to a CPA to answer questions throughout the year and during tax season. The CPA will also perform a final review of your tax return in TurboTax prior to filing. 

The mobile app makes it easy to track mileage while driving and capture photos of receipts for business expenses. Most accounting software is not designed to separate business transactions from personal transactions, but a special feature of QuickBooks Self-Employed provides an option to mark each transaction as business or personal. This is helpful for freelancers who don’t have a separate bank account for their business activity.

BEST FREE SOFTWAREWave


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Wave is an ideal accounting software platform for a service-based small business that sends simple invoices and doesn’t need to track inventory or run payroll. For many freelancers or service-based businesses, Wave’s free features will cover all of their accounting needs and is the best free software in our review. At year-end, accountants can pull the necessary reports from Wave to prepare a business’ tax return.Pros

  • Free accounting, invoicing, and receipt scanning
  • No transaction or billing limits
  • Run multiple businesses in one account
  • Unlimited number of users
  • Mobile app

Cons

  • Limited third-party app integrations
  • Higher fees for credit cards and ACH payments
  • Full-service payroll is limited to only 14 states
  • No inventory management

Wave was founded in 2010 and is based in Toronto. The company has over 250 employees and was purchased by H&R Block in 2019.34 The foundational accounting features that most small businesses need, such as income and expense tracking, financial reporting, invoicing, and scanning receipts, are all included with this free software. These features can be accessed online or on the mobile app. Customer payment processing and payroll are considered premium services that cost extra, but all of the bookkeeping, invoicing, and reporting features are completely free.

Wave makes its money on its payment gateway. To process payment from a customer, Wave charges 2.9% plus 30¢ per transaction for Visa, Mastercard, and Discover, and 3.4% plus 30¢ per transaction for American Express. These fees are slightly higher than other accounting software. Additionally, to process an ACH payment, rather than a credit card, Wave charges 1% per transaction with a $1 minimum fee. This is unique to Wave, as the majority of accounting software does not charge a fee for ACH payment processing. 

Wave offers two payroll plans as an add-on service. The first plan is $20 per month plus $6 per employee or contractor. In this plan, Wave will process payroll and prepare payroll tax calculations, but the user is responsible for manually completing payroll tax forms and submitting tax payments. The second plan is $35 per month plus $6 per employee or contractor. In this plan, payroll is full-service, which means that all tax filings and payments are completely managed by Wave. This full-service payroll option is only available in 14 states.

Conclusion

White label payroll for multiple clients or check with each client to determine what you charge for expenses to do audits.Thomson Reuters Payroll Software, Desktop Payroll Software, QuickBooks Payroll Software are all great options to run your payroll in house. The best option is the one that gives you the best return.

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