The Controller’s Guide to Payroll and Benefits

If you're a controller, you're no stranger to the delicate dance between accuracy and efficiency. You live in spreadsheets, forecast models, and GL codes.

But when it comes to payroll and benefits, even the most seasoned finance pro can feel like they're wading into HR’s backyard with a calculator in one hand and a prayer in the other.

Payroll and benefits aren’t just about making sure everyone gets paid on time, although yes, that’s a very good place to start. It’s about compliance, communication, employee experience, and yes, keeping the auditors happy. In other words, it’s a lot.

So here’s your guide to navigating the world of payroll and benefits from a controller’s perspective—what to focus on, what to watch out for, and how to keep your sanity intact.

1. Payroll Accuracy Is Your Reputation

Let’s start with the obvious. Payroll has to be accurate, every single time. Employees can forgive a lot, but miss a paycheck or mess up a tax deduction and you’ll have more than just a line item to reconcile—you’ll have trust to rebuild.

For controllers, that means tighter coordination with HR, a clear understanding of your payroll provider’s system, and robust internal controls. Automate where you can, but don’t forget the power of a good old-fashioned payroll checklist. Every month, every cycle.

2. Compliance Is Not Optional (Even If It’s Boring)

Nobody enjoys digging through IRS publications or keeping up with state-by-state labor laws. But as the financial steward of your organization, it’s your job to make sure payroll is compliant at every level. Misclassification of employees, misreporting wages, or late filings can cost your company big—and that’s before the reputational damage.

Staying current isn’t glamorous, but it’s necessary. Subscribe to updates from the DOL and IRS, and if your company operates across multiple states, be extra vigilant about local labor laws. When in doubt, ask legal. It’s cheaper than litigation.

3. Partner With HR (They’re Not the Enemy, Promise)

Yes, HR speaks in feelings and you speak in numbers. But payroll and benefits live in the space between the two. Good communication with HR ensures that salary adjustments, bonuses, new hires, terminations, and benefit changes get handled accurately and on time.

Set up recurring check-ins. Share documents. Build a shared calendar for payroll deadlines and benefit enrollment periods. The smoother the communication, the fewer fires you’ll need to put out on payday.

4. Benefits: Where Cost and Culture Collide

Benefits aren’t just an expense—they’re a reflection of your company’s values. As a controller, you’re often the one evaluating the cost side, but don’t overlook the impact benefits have on retention and morale.

Work with HR to evaluate benefit utilization annually. Are people using the offerings? Are there more cost-effective options? Is the broker earning their commission? Treat benefits as a living, breathing part of your budget, not a fixed number. You might be surprised where efficiencies hide.

5. Audit-Proof Your Payroll Process

Auditors love payroll. It’s got everything they crave: repetitive transactions, clear trails, and ample room for error. To make their job easier—and yours less stressful—ensure that every payroll process is documented and repeatable. Approvals should be logged, exceptions tracked, and any manual adjustments clearly explained.

You’ll sleep better knowing you can produce a report or justification within minutes instead of hours.

6. Don’t Underestimate the Power of Technology

Modern payroll platforms can do a lot, but only if you actually use their capabilities. Integrate payroll with your accounting system. Use alerts to catch anomalies. Set up audit trails and approval hierarchies. The more integrated your systems, the less time you’ll spend chasing data or resolving errors.

But here’s the catch: tech only works if the process behind it is solid. Invest the time upfront to align your tech with your workflows. Otherwise, you’re just speeding up a bad process.

7. Plan for Growth, Not Just the Now

If your company is scaling, your payroll and benefits processes need to scale with it. What works for 20 employees won’t work for 200. Review your systems annually and assess whether they can support your projected headcount, complexity, and compliance needs.

Controllers should be asking not just “What does this cost?” but also “Will this still work in two years?” That’s the kind of forward-thinking that makes leadership pay attention.

8. Payroll Is People Work (Even If It Feels Like Math)

At the end of the day, payroll is personal. Every paycheck affects someone’s mortgage, their grocery run, their sense of security. It’s one of the most tangible interactions employees have with your company, and it reflects your commitment to accuracy and care.

Controllers might not get a lot of spotlight for running a flawless payroll, but behind every successful business is a finance leader who gets the numbers right, keeps the rules straight, and quietly makes sure the wheels don’t fall off.

Final Thoughts

Payroll and benefits might not be the most glamorous part of a controller’s job, but they’re among the most impactful. The devil is in the details—but so is the opportunity. A well-run payroll process builds trust, reinforces culture, and supports strategic growth.

And yes, sometimes it also saves your bacon come audit season.