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Payroll Software Features for Small Businesses & CPAs

Discover payroll features built for small businesses and accountants. CheckMark Payroll Solutions gives you the tools to automate payroll, file taxes with confidence, manage employee information, generate essential reports, and stay compliant with changing regulations — making payroll easier from start to finish.

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payroll processing

Run Payroll in Minutes

Process accurate payroll with automated calculations and flexible pay options.

Fast Payroll Processing

  • Process employee pay for hourly, salaried, overtime, bonuses, and commissions
  • Support multiple pay schedules (weekly, bi-weekly, monthly, quarterly)

Automated Payroll Calculations

  • Automatically calculate employee pay
  • Reduce manual errors with pre-configured calculations

Flexible Payroll Adjustments

  • Handle special checks (bonuses, after-the-fact, adjustments)
  • Easily void, edit, or reissue checks
  • Review payroll before finalizing to avoid errors
  • Allocate wages after payroll is processed
Explore Payroll Processing Features
tax compliance

Stay Compliant with Automated Tax Calculations

CheckMark Payroll Solutions handles federal, state, and local taxes for you.

Automatic Tax Calculations

  • Calculate Federal Withholding, Social Security, Medicare, FUTA & SUTA
  • Set up state & local taxes
  • Configure local taxes and custom tax categories

Up-to-Date Tax Tables and Compliance

  • Built-in federal and state tax tables
  • Automatic updates for annual tax changes
  • Assign tax profiles per employee
  • Support for multi-state payroll processing
Explore Tax Compliance Features
employee management

Manage Employees with Ease

Keep employee data, pay settings, and tax information organized in one centralized, secure location.

Centralized Employee Records

  • Built-in federal and state tax tables
  • Automatic updates for annual tax changes
  • Assign tax profiles per employee
  • Support for multi-state payroll processing
  • Add, edit, or remove employees anytime
  • Import employee data to save setup time
  • Track vacation and sick accruals and year-to-date balances

Flexible Pay and Tax Settings

  • Assign multiple pay rates
  • Manage tax filing status, deductions, and additional income
Explore Employee Management Features
employee self service portal

Employee Self-Service Access

Give employees secure access to pay stubs, payroll history, and their information. Available only in CheckMark Online Payroll.

Self-Service Payroll Access

  • Employees log in anytime via the ESS portal
  • View and download pay stubs
  • Access payroll history and earnings details
  • Download year-end tax forms online

Employee Data & Document Management

  • Update personal information
  • Upload onboarding and payroll documents
  • Reduce HR requests and manual tasks
  • Support faster, paperless onboarding
  • Securely store employee documents
Explore Employee Self-Service Features
document management

Organize and Manage Payroll Documents in One Place

Store, access, and manage payroll documents securely without manual work or scattered files.
Available only in CheckMark Online Payroll.

Centralized Document Storage

  • Store employee forms and company records
  • Access files instantly when needed
  • Eliminate paper-based storage

Secure Document Sharing & Control

  • Share documents with employees via the ESS portal
  • Control access and document visibility
  • Update or replace files anytime
  • Maintain accurate and compliant records
Explore Document Management Features
incomes and deductions

Flexible Earnings, Deductions & Benefits

Handle complex payroll scenarios with our simple payroll software.

Additional Income

  • Bonuses, commissions, tips, mileage, piecework
  • Fixed, variable, per-hour, per-period, or % of wages/sales
  • Up to 40 income categories
  • Assign up to 8 additional incomes per employee.

Deductions

  • 401(k), insurance, garnishments, loans
  • Fixed amount or percentage-based deductions
  • Set limits: Annual, monthly, per pay period
  • Employer matching options
  • Up to 60 deduction categories
  • Assign up to 16 deductions per employee.
Explore Incomes & Deductions Features
payroll reports

Powerful 40+ Payroll Reports

Access detailed payroll insights with over 40 built-in reports and summaries for informed decision-making.

Detailed Payroll Reporting

  • Employee earnings and paycheck reports
  • Tax liability and filing reports

Customizable Business Insights

  • Department/job cost reports
  • Income and deduction summaries
  • Employer payment reports
  • Federal, state, and local tax reports
Explore 40+ Payroll Reports
year end tax filing

Simplified Year-End Tax Filing

Generate, review, and file tax forms with built-in reporting tools to ensure accurate year-end payroll compliance.

Generate and File Tax Forms

  • Prepare W-2 and W-3 forms
  • Generate Forms 941, 940, 943, and 944
  • Support electronic filing (EFW2 format)

Year-End Accuracy and Compliance

  • Year-end rollover to new payroll year
  • Built-in compliance checks before filing
  • Handle multi-state reporting & special cases (tips, adjustments, etc.)
Explore Tax Filing Features
employee payments

Pay Employees Your Way

Pay employees via checks or direct deposit with secure and flexible options.

Print Checks

  • Print payroll checks with customizable formats
  • MICR encoding support for professional check printing

Direct Deposit and Digital Payments

  • ACH direct deposit support CheckMark Payroll Solutions generate ACH-formatted files for direct deposit, allowing you to submit them to your bank or web-based deposit service for processing employer and employee payments.
  • Export files for bank processing
  • Email pay stubs to employees
Explore Payroll Payment Features
multi company payroll

Multi-Company Payroll Management for CPAs & Large Businesses

Easily manage multiple companies in one place with our payroll software.

Ideal for Accountants

  • Manage multiple companies in one system
  • Store multiple companies in separate databases for control
  • Easily switch between clients

Efficient Data Management

  • Copy setup data between companies
  • Reduce repetitive setup and save time
Explore Multi-Company Management Features
payroll departments jobs

Track Labor by Department & Job

Allocate wages and track labor costs across departments and projects.

Labor Cost Tracking

  • Create up to 99 departments
  • Assign employees to departments

Advanced Job Costing

  • Track labor costs by department or job
  • Allocate wages across departments or jobs
  • Reallocate wages after payroll processing
Explore Departments & Jobs Features
accounting integration

Payroll and Accounting Integration

Import payroll data into your accounting software to reduce manual work, minimize errors, and streamline financial recordkeeping.

Integrate Payroll with Accounting

  • Post payroll data to popular accounting systems, including CheckMark MultiLedger
  • Map wages, taxes, and deductions

Reduce Manual Work

  • Maintain accurate financial records with less manual work
  • Eliminate duplicate data entry and reduce errors
Explore Accounting Integration Features
data security

Secure and Reliable Payroll Software

Keep your payroll data secure, backed up, and easily accessible. Available with CheckMark Payroll Software.

Data Protection and Backup

Full Control of Your Payroll Data

  • Full control of your payroll files (no forced cloud dependency)
  • Maintain historical data year-over-year
Explore Data Security Features
payroll software proces

Take Control of Your Payroll Today

Join thousands of small businesses and CPAs saving time with CheckMark Payroll Solutions. Start your free trial — no credit card required.

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