An employee’s gross pay is never what they take home. Between taxes (which you can’t avoid) and deductions (which are often voluntary), a 3,200 by the time it hits their bank account. Deductions cover benefits, retirement contributions, garnishments, and anything else that comes out of their pay before or after taxes.Documentation Index
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Deduction types
Pre-tax deductions
These come out before taxes are calculated — meaning they reduce taxable income. Employees pay less in taxes when they use pre-tax benefits.| Type | Common examples |
|---|---|
| Health insurance | Medical, dental, vision premiums |
| HSA contributions | Health Savings Account deposits |
| FSA contributions | Flexible Spending Account deposits |
| 401(k) traditional | Pre-tax retirement savings |
| Commuter benefits | Transit passes, parking |
Post-tax deductions
These come out after taxes are calculated — the employee has already paid income tax on this money.| Type | Common examples |
|---|---|
| Roth 401(k) | After-tax retirement (tax-free withdrawals later) |
| Life insurance | Employer-paid amounts over $50k are taxable |
| Garnishments | Court-ordered child support, tax levies, creditor judgments |
| Union dues | If applicable |
| Charitable donations | Payroll giving programs |
Setting up deductions
Company-level setup
First, create the deduction types your company offers:Configure it
- Name (e.g., “Medical Insurance - Employee”)
- Pre-tax or post-tax
- Category (health, retirement, other)
- How to calculate (fixed, percentage, per hour)
Employee-level assignment
Each employee opts into (or is assigned) specific deductions:- Open the employee’s profile
- Go to Deductions
- Click Add Deduction
- Select the type and enter their specific amount
- Save
Calculation methods
| Method | How it works | Example |
|---|---|---|
| Fixed amount | Same dollar amount each period | $200/paycheck for health insurance |
| Percentage | Percent of gross pay | 6% of gross to 401(k) |
| Per hour | Amount times hours worked | Union dues at $0.50/hour |
| Annual limit | Stops when limit is reached | 401(k) stops at $23,000 |
Percentage example
Employee contributes 6% to 401(k):- Gross pay this period: $5,000
- 401(k) deduction: $300
Annual limits
The IRS caps certain deductions:| Type | 2025 Limit |
|---|---|
| 401(k) traditional/Roth | 30,500 if 50+) |
| HSA (individual) | $4,150 |
| HSA (family) | $8,300 |
| FSA | $3,200 |
Employer contributions
Many benefits include an employer contribution:| Benefit | Typical employer contribution |
|---|---|
| 401(k) | 50% match on first 6% (employee contributes 6%, you add 3%) |
| HSA | Fixed amount per month ($50-100 common) |
| Health insurance | 50-80% of premium |
Garnishments
You just received a court order requiring you to withhold money from an employee’s paycheck. This isn’t optional.Add the garnishment
Set up the deduction with:
- Type (child support, tax levy, creditor judgment)
- Amount or percentage (as specified in the order)
- Maximum per pay period (some have caps)
- End date (if the order specifies one)
Garnishment priority
When an employee has multiple garnishments, federal law dictates the order:- Child support — always first
- Tax levies — IRS and state tax
- Other creditors — credit cards, judgments, etc.
Effective dates
Deductions can be scheduled:- Start date — When the deduction begins (new hire, open enrollment)
- End date — When it stops (employee leaves plan, garnishment satisfied)
- Change effective date — When an amount change takes effect
Reports
Track what’s being deducted:| Report | What it shows |
|---|---|
| Deduction summary | All deductions by type and employee |
| Benefit costs | What benefits are costing you (employer portions) |
| Garnishment register | Active garnishments and payments made |
| 401(k) contributions | For sending to your plan administrator |
Direct deposit
Get paychecks into employee bank accounts.