Should my accountant run payroll or a payroll service?

Short answer: it depends on what you need payroll to do

If your accountant already runs payroll correctly, on time, and with clear communication, that can work well for your business.

A dedicated payroll service can be a better fit when you want payroll to run on schedule automatically, including pay runs, direct deposit, and help with W-2/1099 work—often with simpler, more consistent payroll support.

The key is not “who is doing it,” but whether the person or service handles the full payroll workflow reliably in your situation and can prove (in writing) what they do.

RunWise Pay is a FREE matching service—not a payroll provider or tax advisor. We help small and mid-size businesses compare payroll services that run payroll and handle payroll taxes and year-end forms. The provider you choose stays in charge of pricing and details.

How payroll is usually handled in the US (plain-English basics)

In the US, payroll isn’t just paying employees. Payroll typically includes calculating wages, withholding required taxes, filing payroll tax reports, paying employees (often by direct deposit), and producing year-end forms like W-2s and 1099s.

When payroll is outsourced to a payroll service, the service generally manages the pay runs and the tax filings, based on federal and state rules. An accountant may do some payroll work too, but many accountants prefer to manage the accounting side (books, taxes) while a payroll service manages the operational payroll details.

There are also hybrids: some businesses have payroll prepared by one party and bookkeeping/tax planning handled by another. None of this is “wrong”—the best choice is the one that fits your payroll complexity and your team’s ability to manage deadlines.

Questions to ask before you decide (accountant vs. payroll service)

1. What exactly will be handled? Ask for a clear checklist: pay runs, tax calculations, payroll tax filing, employee pay by direct deposit, and year-end forms (W-2/1099).

2. Who updates pay and tax details when something changes? For example: new employees, pay rate changes, benefits, garnishments, or state changes.

3. What is the cutoff schedule? Payroll has deadlines. Confirm the time you must submit hours/pay changes and how late changes are handled.

4. What support do you get when there’s an error? Ask what the process is if an employee says the pay looks wrong, a tax filing needs correction, or a year-end form has an issue.

5. Will you receive written confirmation of what’s included? Before you sign anything, confirm what the provider/accountant will do in writing (deliverables, responsibilities, and deadlines).

• - If your accountant runs payroll, ask whether they also file payroll taxes and produce W-2/1099 forms, or if another party does that.
• - If you use a payroll service, ask whether your accountant still prepares taxes/financial statements and how they share information.

Cost reality: what you might pay (and what changes the price)

Pricing varies a lot by company size, pay frequency, state, and what’s included (for example: direct deposit, tax filing, year-end forms, support, and reporting). Because of that, any “typical range” is not a quote.

A common structure for payroll services is a base monthly fee plus an additional per-employee fee. As a rough guide, many small businesses see monthly pricing that can start around a few dozen dollars per month and go higher depending on how many people they pay and how often they pay them. Some setups may cost more if you need extra processing (for example, converting from another system).

If your accountant runs payroll, some accountants bundle payroll into their overall accounting package, while others charge separately. Either way, ask for the full, written pricing terms and what happens if you add employees or change pay frequency.

If fees come up, focus on total cost and inclusions—not unclear wording. And remember: RunWise Pay is FREE for business owners to use; participating providers pay to be matched.

Payroll red flags to watch for (regardless of who runs it)

Be careful if pricing is vague. For example: “we handle payroll” without listing what’s included (tax filings, year-end forms, support, correction process) can lead to surprise bills later.

Avoid providers/accounting arrangements that don’t clearly explain deadlines and responsibilities. If you can’t confirm when you must submit hours and who fixes problems when something goes wrong, that’s a risk.

Watch out for these common pressure tactics: being rushed to sign quickly, refusing to put key details in writing, or giving verbal assurances instead of a written scope of work.

Most importantly: confirm what’s included in writing—what they do, what they don’t do, and what you must provide. If you’re unsure, ask questions until the responsibilities are clear.

How to get matched to a payroll service (free) and compare options safely

If you want a payroll service that can handle the operational payroll tasks, you can use RunWise Pay to compare options. It’s a FREE matching service—not a payroll provider—so you stay in control of the final decision.

Here’s how it works in practice:
1. Tell us your business intent and basics (business name, contact name, phone, optional email, your state, how many people you pay, and preferred language).
2. We connect you with participating payroll service providers that handle businesses like yours.
3. You review responses, compare written inclusions and costs, and choose who to hire.

Safety note: we only collect contact + business intent details. We do not ask for SSNs, EINs, bank account numbers, or employee records. When you talk to a provider, share only what they request through their normal, secure process.

Next steps: explore guides for payroll basics, see services to understand typical payroll responsibilities, and start the match at get-matched.