Best Payroll Services in San Diego, CA

Updated: December 22, 2023

We sifted through the best payroll services in San Diego to help you pinpoint the perfect one for your business.

Payroll services are real life-savers for businesses in San Diego. They help you save time, make sure you’re staying compliant, boost payroll accuracy, and improve employee satisfaction. It's a total win-win situation.

Patriot logo

Free onboarding

Free Trial
Gusto logo
Best Pick

Next-day direct deposit available

Get Started
SurePayroll logo

Backed by Paychex

Get Started

Compare the best payroll companies in San Diego

In Sunny San Diego, we've got no shortage of payroll service providers. We did the legwork for you by comparing services offered, integrations, cost, reputation, customer service, and more to help you make the best choice. Here's our shortlist of the best payroll companies in San Diego we'd recommend.

Company NameGustoPatriotSurePayroll
Best forSMBs, freelancers, contractorsAffordable, easy payrollSimple small business payroll
Years in Business112123
Starting Price$40/month + $6/mo per person$17/month + $4/mo per person$29.99/mo + $5/mo per person
Direct Deposit
Tax ComplianceMulti-State, FederalMulti-State, FederalMulti-State, Federal
B2B Reviews Rating4.84.84.7
ReviewsRead ReviewsRead ReviewsRead Reviews

San Diego's Best Payroll Companies



Editorial Rating

Gusto logo
  • Benefits management options
  • High-level customer service
  • Next-day direct deposit available
  • Best Overall

Gusto is a cloud-based platform that's a real game changer for small businesses, handling all your payroll and benefits needs. It's got everything you need, from running payroll, to dealing with taxes and filing those tricky tax forms. With Gusto, San Diego businesses can handle benefits, like health insurance and 401(k) plans, without breaking a sweat. Plus, employees get self-service tools to manage their own info.

Gusto's super easy-to-use interface, its ability to play nice with other software, and flexible pricing options make it a big hit with small business owners. Plus, they've got top-notch customer support and they'll help you make sure you're following all the payroll rules. It's a solid choice.



Editorial Rating

Patriot logo
  • One of the cheapest options
  • Easy setup
  • Free onboarding
  • Excellent customer service

Patriot's budget-friendly payroll service is perfect for small businesses with simple payroll needs. It offers super user-friendly software that lets San Diego businesses run payroll fast and without any hiccups. Plus, Patriot offers direct deposit, helps you keep on top of tax rules, and lets you customize your payroll reports.

With Patriot, your employees can manage their own info through a self-service portal, and the platform plays well with other software, like QuickBooks. All in all, if you're a small business in San Diego and you just need the basics when it comes to payroll, Patriot's a great bang-for-your-buck choice.



Editorial Rating

SurePayroll logo
  • Free 2-day direct deposit
  • HR advisor included
  • Backed by Paychex
  • Tax filing service available

SurePayroll is a solid, wallet-friendly payroll solution for small businesses that need to handle payroll processing, stay on the right side of compliance, and give employees self-service tools. It's got an easy setup, a secure online portal, and lets employees manage their own payroll info.

With SurePayroll, businesses get the benefit of automatic tax filings, tracking time and attendance, and pricing that won't break the bank. They even have a mobile app so you can handle payroll when you're out and about, plus round-the-clock customer support for any payroll questions or worries you might have.


Pink Payroll

    4010 Morena Blvd, Ste 220
    San Diego CA 92117

    Phone: (858) 217-5802

    Pink Payroll offers customized payroll services, employee benefits, and pay-as-you-go workers’ compensation for businesses in San Diego and the surrounding area as well as all 50 states. Between timekeeping, paycheck delivery, direct deposit, and electronic reporting, Pink Payroll pretty much does it all when it comes to outsourcing HR and payroll for your business. The firm will also help you with payroll tax deposits and filing, employment screening, employee onboarding, and more. You can request a custom quote through the online form on the company’s website.


    Payroll Vault San Diego South Bay

      Phone: (858) 967-0417

      Payroll Vault provides HR solutions and payroll services for businesses in San Diego, Chula Vista, El Cajon, National City, La Mesa, Coronado, Imperial Beach, Lemon Grove, and the surrounding area. Payroll Vault is a local business partner offering timekeeping, hew hire reporting, retirement plan reporting, payroll processing, background screening, quarterly filing for state, local, and federal taxes, employee and employer portals, and much more. You must request a quote for pricing.


      Business Payroll Services Inc.

        804 N Twin Oaks Valley Road Suite 119
        San Marcos, CA 92069

        Phone: (866) 949-4807

        Business Payroll Services is headquartered in Southern California and has offices in San Diego, CA and Dallas, TX. Employee and manager self-service portals, timekeeping and attendance tracking, full-service payroll and tax filing, and HR outsourcing are some, but not all, of what Business Payroll Services offers. Request a free quote online and get free labor law posters with your free consultation.


        Coastal Payroll Services

          9350 Waxie Way, Suite 110
          San Diego, CA 92123

          Phone: (858) 565-2123

          Coastal Payroll launched in 2007 and provides local payroll services and human capital management for thousands of clients in California and nationwide. They offer a full range of HR services and have offices in San Diego, Orange County, and the Bay Area. Coastal Payroll’s core payroll services include payroll processing, payroll reporting, benefit accruals, garnishment management, and tax management. You can complete the form on their website to request a quote.

          How do payroll services work in San Diego?

          Payroll services work in San Diego, California much the same way they do anywhere else in the United States. Here’s a basic breakdown of how they function:

          • Kickoff: First, you get your business all set up with the payroll service. You’ll need to hand over some details about your company, like your EIN from the IRS, plus info about your team members: their Social Security Numbers, salaries, or hourly rates, and all that good stuff.
          • Staying Current: You need to keep your payroll service provider in the loop with updated info on work hours, any overtime, bonuses, and the like. You can send this weekly, every two weeks, or monthly.
          • Figuring Out the Pay and Deductions: Here’s where your payroll service earns its keep. They’ll calculate each of your employees’ gross pay from the info you provide, then they’ll work out all the deductions. We’re talking federal, state, and local taxes (including our very own San Diego local tax rates), as well as deductions for things like health insurance, 401(k) contributions, wage garnishments, and so on.
          • Making it Rain: Come payday, your payroll service gets your employees paid. They can do direct deposit right into your employees’ bank accounts, cut a paper check, or load up a payroll debit card.
          • Taking Care of Taxes: Your payroll service will also handle all the tax stuff related to payroll. They make sure your payroll taxes get paid to the right tax agencies and they’ll file your quarterly or annual payroll tax returns.
          • Keeping Tabs: Lastly, your payroll service will keep track of all your payroll transactions and will send you reports. This is a big help for your own record-keeping, and it’s a must-have for stuff like audits or if you’re looking to get a business loan.

          And remember, here in San Diego, just like everywhere else in California, there are state-specific labor laws that impact payroll. That includes minimum wage, overtime rules, and paid sick leave laws. A good payroll service will help you navigate these regulations and make sure you’re all compliant.

          How much do payroll services cost in San Diego?

          The cost of payroll services can vary greatly depending on the specific services you need, the number of employees you have, and the provider you choose. Here are some general ranges:

          Basic Payroll Services: If you’re just looking for the nuts and bolts – figuring out pay and taxes, getting checks printed and delivered, and maybe some basic reports – you’re probably looking at something like $20 to $100 a month, plus a couple of bucks to maybe $15 per employee. This’ll depend on who’s doing your payroll and what exactly they’re doing for you.

          Full-Service Payroll: Now, if you need the full monty – that’s direct deposit, reporting new hires, filing taxes, and better reports – you could be dropping anywhere from $50 to $200 or more every month, plus an extra per-employee fee.

          Additional Services: Some payroll providers offer additional services like HR support, tracking time and attendance, handling benefits, and more. This is gonna cost you extra, and the prices can vary widely.

          Remember, these are just ballpark figures, and what you’ll actually pay can be different. We recommend getting pricing from a few different payroll providers to see what they charge for what you need. Also, think about the time and headaches you’ll save by having someone else handle payroll, plus the peace of mind knowing it’s in good hands. A lot of times, the cost of a payroll service pays for itself when you consider all that.

          Patriot logo

          Free onboarding

          Free Trial
          Gusto logo
          Best Pick

          Next-day direct deposit available

          Get Started
          SurePayroll logo

          Backed by Paychex

          Get Started

          Payroll laws in California

          Payroll laws in California are among the most complex in the U.S., encompassing minimum wage requirements, overtime rules, meal and rest breaks, and more. Below are some key points to know:

          Minimum Wage

          As of 2024, the minimum wage in California is $16.00 per hour for all employers. However, some cities have higher minimum wages than the state’s rates.


          California has stricter overtime laws than many other states. Employees are entitled to 1.5 times their regular rate of pay when they work over 8 hours in a day or 40 hours in a week. They are also entitled to this rate for the first 8 hours they work on the 7th consecutive day of work in a workweek. Double time is owed for hours worked over 12 in a day or over 8 on the 7th consecutive day.

          Meal and Rest Breaks

          Employees are entitled to a 30-minute unpaid meal break if they work more than 5 hours in a day. They also get a paid 10-minute rest break for every 4 hours worked.


          Employers must establish regular paydays and provide notice of these to their employees. Wages earned between the 1st and 15th of the month must be paid by the 26th, and wages earned between the 16th and the end of the month must be paid by the 10th of the following month.

          Final Paychecks

          If an employee is fired or laid off, they are entitled to receive their final paycheck immediately. If an employee quits without giving 72 hours’ notice, the final paycheck is due within 72 hours. If they provide 72 hours’ notice, the final paycheck is due on their last day.

          Pay Stub Requirements

          California law requires employers to provide itemized wage statements that include certain information, such as gross wages earned, total hours worked, all deductions, net wages earned, pay period dates, and the employee’s name and last four digits of their Social Security number.

          These laws are enforced by the California Department of Industrial Relations. Employers who fail to comply with California’s payroll laws may face penalties. It’s also worth noting that employers in San Diego, like other cities in California, may be subject to local ordinances that provide even greater protections to workers. Employers should consult with a legal or HR professional to ensure full compliance.

          The Bottom Line

          By picking the right payroll service, San Diego small businesses can get more accurate and compliant, spend less time on paperwork, and get a better picture of their labor costs. Plus, lots of payroll services offer extra HR perks like onboarding, benefits management, and time and attendance tracking, which can make your HR operations run smoother and save you some serious time and cash.

          Whether you’re a small biz or a growing outfit, payroll services can give you a real boost in managing your HR and payroll tasks. By going with a reliable provider that gets the unique needs of your San Diego business, you can make sure your payroll processing is on point and compliant, and spend more time focusing on growing your business.

          The methodology behind our rankings

          Here are the key factors we considered when selecting the best payroll service providers for businesses in San Diego, CA

          • Services offered: We scoped out payroll companies that bring all the goods to the table, like handling the payroll, filing taxes, setting up direct deposit, and giving employees access to handle their own info.
          • Cost: We did a price check on different payroll service providers to find ones that wouldn’t break the bank. We gave bonus points to companies that have flexible pricing, letting you scale up or down depending on your business size and needs.
          • Reputation and experience: We wanted payroll providers that have a solid rep and plenty of years under their belt. We took a look at what customers had to say by checking out reviews and testimonials to get a feel for how reliable they are and how they treat their customers.
          • Technology: We picked out payroll service providers that stay current with the latest tech that can make payroll a breeze and give you online access to all your payroll data.
          • Compliance: We made sure the payroll companies we picked know their stuff when it comes to federal and state payroll laws and regulations and stick to them like glue.
          • Customer support: We wanted payroll service providers that have top-notch customer service, ready and able to handle any questions or issues you might have, and get back to you quick.
          • Scalability We went for payroll service providers that can handle businesses of all sizes and are ready to grow with you as your business takes off.
          • Integrations: We gave props to payroll service providers that can play nice with other business software, like accounting or time tracking, to streamline your processes and keep errors to a minimum.