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Payroll Deduction Software to Manage Employee Earnings & Deductions

Managing payroll deductions accurately is essential for every business. From employee tax deductions and payroll taxes to benefits, bonuses, and reimbursements, CheckMark Payroll Solutions makes it easy to calculate deductions, track earnings, manage benefits, and stay compliant.

Handle Any Type of Employee Earnings

Go beyond basic wages with powerful additional income management. With CheckMark Payroll Solutions, you can create and manage:

  • Bonuses and commissions
  • Tips (reported and allocated)
  • Mileage reimbursements
  • Piecework and production-based pay
  • Custom income types specific to your business

You can define up to 40 additional income categories for your company and 8 additional income categories per employee, giving you the flexibility to match any compensation structure.

Handle Every Type

Flexible Calculation Methods for Earnings

Every type of income is calculated differently, and your payroll deductions software should support that. Choose from multiple calculation methods:

Flexible-Calculation Methods Earnings
  • Variable amounts (different each pay period)
  • Fixed amounts per pay period
  • Per hour worked
  • First check of the month or quarter
  • Percentage of wages or sales
  • Mileage-based or piece-rate calculations

This ensures accurate payroll regardless of how employees are paid.

Smart-Tax Handling

Smart Tax Handling for Every Income Type

Different earnings are taxed differently, and CheckMark handles that for you.

  • Define tax treatment for each income type
  • Mark earnings as exempt from: Federal tax, Social Security, Medicare, and state or local taxes
  • Automatically apply correct tax rules for: Reported tips, allocated tips, and special compensation

Stay compliant while handling complex pay structures.

Powerful Payroll Deductions

Powerful Payroll Deductions Management

Easily manage all types of employee deductions with full control. Set up payroll tax deductions for:

  • Retirement plans (401(k), etc.)
  • Health insurance and benefits
  • Garnishments and wage attachments
  • Loan repayments
  • Custom business-specific deductions

You can define up to 60 deduction categories for your company and assign up to 16 deductions per employee.

Flexible Deduction Calculation Options

Handle deductions exactly how your business requires:

  • Fixed amount per pay period
  • Percentage of wages
  • Per hour worked
  • Monthly or quarterly deductions

Choose how deductions apply: Total wages, taxable wages, and disposable income. Built to support real-world payroll rules and compliance requirements.

Flexible-Deduction Calculation

Set Limits & Control Deduction Rules

Avoid over-deductions and stay compliant with built-in controls:

Set Limits Control Deduction
  • Annual limits
  • Monthly limits
  • Per-pay-period limits
  • Loan balance tracking
  • Annual deduction caps

Automatically stop deductions when limits are reached; no manual tracking needed.

Employer-Matching

Employer Contributions & Matching

Support employer-paid benefits and contributions:

  • Configure employer matching (e.g., 401(k))
  • Define fixed or percentage-based contributions
  • Track employer expenses alongside employee deductions

Keep benefits accurate for both employees and accounting.

Earnings Deductions Employee

Customize Earnings & Deductions Per Employee

Every employee can have a unique payroll setup:

  • Assign specific income types to individuals
  • Customize deduction amounts or percentages
  • Override default values when needed
  • Adjust settings without affecting other employees

Total flexibility without disrupting your payroll system.

Adapt to Changes Without Disruption

Payroll needs change, and your system should keep up.

  • Modify income or deduction amounts anytime
  • Add new categories mid-year
  • Adjust rates without rebuilding payroll setup
  • Maintain accuracy across all payroll runs

Stay agile as your business evolves.

Adapt-Changes Without Disruption

Why Businesses & CPAs Choose CheckMark

Payroll is more than paying employees. It’s managing additional incomes, benefits, and payroll deductions accurately. From bonuses and commissions to employee tax deductions, even small errors can impact compliance and employee trust.

CheckMark Payroll Solutions simplifies payroll deduction management, offering flexibility to handle employee tax deductions, benefits, retirement contributions, and wage garnishments with ease and accuracy.

  • Trusted by Businesses Since 1984
  • 40+ Years of Payroll Experience
  • Built for Small Businesses & Accountants
  • US-Based Support from Real Payroll Experts
  • Reliable Payroll Solutions Designed to Grow with You
  • Transparent pricing, no hidden charges

Choose the Right Payroll Deductions Software for Your Business

CheckMark Payroll Software

CheckMark Online Payroll

Best for flexibility, automation, and managing payroll from anywhere.

  • Run payroll online in minutes from anywhere, anytime
  • ACH direct deposit and printed checks
  • Employee Self-Service Portal for pay stubs, tax forms, and payroll documents
  • Automatic payroll tax calculations and tax filing support
  • Year-end W-2 and payroll tax form filing
  • Fast payroll processing for hourly and salaried employees
  • Designed for small businesses and growing teams
Get Started with Online Payroll
Try it Free for 14 Days
CheckMark Payroll Software

CheckMark Payroll Software

Best for data control, advanced payroll processing, and desktop flexibility.

  • Unlimited employees and unlimited payroll runs
  • Process payroll on Mac or Windows desktop
  • Print MICR payroll checks on blank check stock
  • ACH direct deposit file creation
  • Create and manage multiple incomes and deductions
  • Built-in federal and state payroll tax tables
  • Track sick time, vacation accrual, and PTO balances
  • Secure local data storage with optional CheckMark Cloud Backup
Download Desktop Payroll Trial
Try it Free for 60 Days

What Businesses Like Yours Have to Say About CheckMark

inverted commas CheckMark Payroll Software

It is the easiest payroll program I've used…

I have used CheckMark Payroll Software since 2013 for our company's payroll and W-2's. It is the easiest payroll program I've used. I don't need to use the customer support very often, but when I do they are very knowlegable and helpful. We pay commissions and hourly with several income categories and deduction types. Creating the tax reports through the program is very simple also. I highly recommend Checkmark Payroll and 1099 programs.

Sherry, Texas

inverted commas CheckMark Payroll Software

I feel it is efficient and time saving…

I personally am very satisfied with CheckMark Payroll. I feel it is efficient and time saving; especially after using the Federal and State employment tax booklets to look up each deduction for each employee-very antiquated for sure!!! Very easy updates from year to year also.

Christine, New York

Take Control of Your Payroll with CheckMark

Simplify even the most complex payroll deduction scenarios with CheckMark, the flexible and powerful payroll software for small businesses and CPAs.

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