Service
Payroll Bookkeeping Services
Pay your team correctly, every cycle. W-2 and 1099 aware. Deposit-deadline aware.
- AIPB Certified
- QuickBooks ProAdvisor
- Xero Partner
- US-based team
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Payroll is the part of small business bookkeeping that keeps owners awake. The team has to be paid right, on time, with the correct federal and state tax withholding, the correct overtime calculation, and the right classification between employee and contractor. Get any of those wrong and the consequences land on the owner, not the bookkeeper.
We run payroll for businesses with 1 to 20 staff. W-2 and 1099 classification is handled correctly from day one, federal and state payroll tax deposits are tracked against your specific deposit schedule, and overtime is calculated the way the Fair Labor Standards Act and your state's wage and hour rules expect.
What that means in practice: paychecks go out on the right day, payroll tax deposits land before the deadline, year-end W-2s and 1099-NECs go out by January 31, and if the Department of Labor or a state agency ever asks, the records are there.
Where payroll bookkeeping actually helps
- I am running payroll in a spreadsheet and praying I have the withholding rightPayroll moves into Gusto or QuickBooks Payroll with tax tables loaded. Withholding calculations stop being guesswork.
- I keep missing payroll tax deposit deadlines and I am worried about IRS penaltiesDeposits tracked against your specific schedule, semi-weekly or monthly, with reminders well ahead of the deadline.
- I do not understand the difference between a W-2 employee and a 1099 contractor for my teamWe assess each worker against the IRS classification factors and give you a clear answer, in writing, for each one.
- My tipped staff make the overtime math confusing and I am not sure I am calculating it rightTip credit, tip pooling, and overtime on the regular rate are calculated correctly, every cycle, under the FLSA.
- I have workers in two states now and I do not know what that means for payroll taxWe register you for state payroll tax where required and track filings for each state your employees actually work in.
Classification, deposits, overtime. The three things that go wrong in payroll
Most payroll problems we see at onboarding fall into three categories. Workers classified as 1099 contractors when the IRS factors point to employee status (a costly mistake if caught later). Payroll tax deposits paid late, which triggers IRS penalties that scale with how late and how much. And overtime calculated on the base rate only, missing the requirement to fold in tips, bonuses, and shift differentials under the FLSA regular-rate rules.
Onboarding addresses each of those at week one. We walk through every worker and classify them properly against the IRS 20-factor test. We confirm your deposit schedule (semi-weekly or monthly, based on your lookback period) and set up tracking so deposits happen with days of buffer, not on the deadline. We rebuild the overtime calculation so it reflects the actual regular rate, not just the hourly wage.
Each January we handle year-end: W-2s and 1099-NECs prepared and ready to issue by the January 31 deadline, Form 941 reconciled for the year, Form 940 (FUTA) prepared. The work happens behind the scenes; you see one short note explaining what's due and when.
How payroll bookkeeping with Bookflexy runs
Step 1
Discovery call (15 min)
Tell us how many staff, W-2 or 1099, what software you're on, and how you currently run pay. We size the work on the call.
Step 2
Payroll onboarding
We set up or migrate your payroll, confirm worker classification, validate your deposit schedule, and run a test pay before going live.
Step 3
Each pay cycle
Pay run prepared, reviewed, and processed on the agreed schedule. Tax deposits tracked. Pay stubs out same day.
"Wages, tip reporting, casual staff, daily POS reconciliations. I'd been doing it myself between services. They took it off me three months ago and I got my Sundays back. The kitchen noticed I was less on edge. I noticed too."
Why US small businesses choose Bookflexy for payroll bookkeeping
W-2 and 1099 expertise
Worker classification is one of the most commonly mishandled parts of small business payroll. We assess each worker against the actual IRS factors, not a rule of thumb.
Deposit deadlines tracked
Federal and state payroll tax deposits tracked against your specific schedule. The deadline is treated as non-negotiable, because IRS penalties for late deposits scale fast.
Workers' comp aware
Workers' compensation reporting requirements vary by state. We track what your state requires and keep the reporting current alongside payroll.
Multi-state payroll aware
Employees working from different states trigger separate state payroll tax registrations. We handle the registration and ongoing filing for each state you actually have workers in.
Confidential payroll handling
Pay rates and individual records are restricted to the payroll lead on your account. Your other team members do not see each other through us.
Year-end done on time
W-2s and 1099-NECs prepared and ready to issue by January 31. Form 941 reconciled for the year. No scrambling in the first weeks of January.
Get payroll off your weekend
Classification, deposits, overtime, year-end. Tell us your headcount and pay frequency and we will quote it inside a day.
Four payroll shapes
Cafe, restaurant, or bar with tipped staff
Tip credit and tip pooling under the FLSA. Overtime calculated on the regular rate including tips. Split shifts and shift differentials. One of the most commonly miscalculated payroll setups in small business.
What changes
- Tip credit applied correctly against minimum wage
- Tip pooling tracked per FLSA rules
- Overtime on the true regular rate, not just base pay
- State-specific tipped minimum wage rules applied
How small businesses run payroll
Owner runs spreadsheet 1-3 staff, risky | Owner uses payroll software 3-10 staff, requires time | In-house payroll admin 10+ staff, $55k+/year | Outsourced (us) Any size, predictable cost | |
|---|---|---|---|---|
Federal/state deposit tracking | No | Yes | Yes | Yes |
Worker classification review | Manual, error-prone | Manual, error-prone | Skill-dependent | Yes |
Deposits made on time, every cycle | Partial | Partial | Yes | Yes |
Coverage when sick or on leave | No | No | No | Yes |
Predictable cost | Hidden time | Software fees + your time | Salary + on-costs | Fixed retainer |
FLSA-compliant recordkeeping | Partial | Partial | Yes | Yes |
Scales without rehiring | No | Partial | No | Yes |
How pricing works for payroll bookkeeping
Payroll pricing scales with headcount, frequency (weekly versus biweekly versus monthly), and complexity. A weekly hospitality payroll with tipped staff and a mixed W-2/1099 crew carries more work than a monthly payroll with two salaried employees. The quote reflects that.
The form lets you tell us roughly how many staff, the pay frequency, and the mix of W-2 and 1099 workers. The number we send back covers payroll processing, deposit tracking, pay stubs, and year-end prep. Multi-state registration is priced separately when applicable.
Pricing factor
Headcount
Number of workers on payroll. We size from current headcount and adjust at six-month re-scopes if you grow.
Pricing factor
Pay frequency
Weekly is most expensive per pay run because it runs four times a month. Biweekly is the most common. Monthly is the lightest.
Pricing factor
W-2/1099 mix
A heavier 1099 mix shifts work toward classification review and year-end 1099 volume rather than ongoing payroll processing.
Pricing factor
Tipped or hourly mix
Tip credit calculations and hourly overtime reviews add more per-cycle work than salaried payroll.
Pricing factor
Reimbursements and benefits
Tool allowances, mileage reimbursement, 401(k) contribution tracking. Each adds set-up and ongoing review.
Pricing factor
Multi-state payroll
Employees working in more than one state add registration and filing work for each additional state, priced separately.
Your first 90 days
Week 1
Payroll onboarding
Worker classification confirmed, employees set up, deposit schedule validated, PTO balances reconciled, test pay run completed.
Pay run 1
First live pay run
Live pay processed under the agreed schedule. Pay stubs out. PTO accrued.
Quarter 1
First payroll tax deposits
Federal and state deposits made on schedule, with days of buffer before each deadline.
Year-end
W-2s and 1099s ready
Year-end forms prepared and ready to issue by January 31. Form 941 reconciled for the year.
Industries we work with
What clients say
"Wages, tip reporting, casual staff, daily POS reconciliations. I'd been doing it myself between services. They took it off me three months ago and I got my Sundays back. The kitchen noticed I was less on edge. I noticed too."
"I started doing residential, picked up two commercial contracts, and suddenly I had an employee and a 1099 helper. The payroll side scared me. They set it up, ran the first three pay cycles for me, and now I just do the work."
Payroll Bookkeeping FAQ
Two things to remember
Every account is reconciled and kept tax-ready by an AIPB-certified bookkeeper. Every account is run inside the US, by a US-based bookkeeper. Those two facts shape almost every other decision on this page.
Keep exploring
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Industry
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POS reconciliation, tip reporting, supplier invoices.
Industry
Construction
1099-NEC, retainage, progress claims, sub payments.
Get payroll off your plate.
W-2, 1099, deposits, overtime, year-end forms. Tell us your headcount and pay frequency, we will quote it.