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Top Rated Billing and Invoicing Software with Payroll Management in 2026

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Verified reviewer profile picture

All user reviews are verified by in-house moderators and provider data by our software research team.  Learn more

Last updated: April 2026

Payroll management streamlines the entire payroll process including calculations, direct deposits, tax filings, and generating pay stubs. It ensures timely and accurate payments, reduces manual entry, and maintains compliance with tax regulations. Our reviewers in billing and invoicing software rated this feature as highly important.

4 Best Billing and Invoicing Software with Payroll Management

  • FreshBooks - Highest rated for payroll management
  • QuickBooks Enterprise
  • QuickBooks Desktop
  • QuickBooks Online

See other top Billing and Invoicing products with payroll management

How we picked the 4 top rated products

We chose the high-performing solutions on this list based on verified user ratings on our site. Depending on available data, qualifying products either had to be among the most user-reviewed or the most searched-for products in the billing and invoicing software category. They also needed to have sufficient reviews about payroll management, have a minimum user rating of 3 out of 5 for that feature, and show evidence of U.S. market presence. We then added a distinction for the product with the highest rating for payroll management based on our proprietary ratings and reviews. Sponsorship or client status has no influence on the selection of these products, but it may impact the order in which products appear.

Details for the 4 best products

FreshBooks logo
4.5
(4.5K)

User insights about the payroll management feature

Reviewers appreciate FreshBooks' payroll management capabilities, noting its ease of use and time-saving aspects. They highlight the ability to manage payroll for large numbers of employees and the accuracy of payroll calculations. Users also value the integration with third-party payroll providers like Gusto and Wagepoint, which ensures accurate and timely payments. They find the intuitive layout and bulk upload feature particularly helpful for streamlining payroll processes.
“It's important to note that Freshbooks is primarily a cloud accounting software for small business owners, and it does not offer a built-in payroll management feature. Freshbooks allows you to create and send invoices, track expenses, manage accounts receivable and accounts payable, and generate financial reports, among other features. However, if you need a payroll management system, you would need to integrate Freshbooks with a third-party payroll provider. Freshbooks integrates with a variety of popular payroll providers, such as Gusto and Wagepoint, which offer features such as calculating and filing payroll taxes, direct deposit, and employee self-service portals. By integrating Freshbooks with a payroll provider, you can streamline your payroll management process and ensure that your employees are paid accurately and on time.”
IZ

Idris Z.

Content writer

“ Enables accurate payroll calculations by synchronizing employee time entries and expenses.”
SM

Stephen M.

Managing Director

Billing and Invoicing key features coverage

FreshBooks offers 6 out of the 6 key features for Billing and Invoicing software identified by reviewers:

Invoice Processing4.6
Invoice Creation4.6
Online Invoicing4.6
Invoice History4.6
Payment Processing4.5
Tax Calculation4.6

Pros and cons based on 4,506 verified reviews

59% of users rated FreshBooks 5 out of 5 stars, while 2% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 4,506 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Cloud accounting accessibility

Efficient invoicing capabilities

Tailored for small businesses

Minimal learning curve

Effective freelancer tools

Cons:

Reliance on internet connection

Limited bank integration

High costs for larger teams

Frequent technical issues

See pros and cons details

Pricing

Starting price:$21 flat rate/per month|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

QuickBooks Enterprise logo
4.5
(20.6K)

User insights about the payroll management feature

Reviewers indicate that QuickBooks Enterprise simplifies payroll management with features like automated calculations, tax filings, and paycheck generation. They find it easy to use and appreciate the ability to manage employee data and payroll taxes efficiently. Users report that it helps ensure timely and accurate payments, although some mention the need for improvements and occasional glitches. The integration with other financial functions is also valued for comprehensive payroll management.
“Comprehensive payroll management feature that helps companies streamline their payroll process. With QuickBooks Payroll, users can easily manage employee data, calculate and file payroll taxes, and create payroll and payroll checks.”
MK

Mehdi K.

Mehdi work

“Quickbooks does it all; generate paychecks, pay payroll taxes, do reports. No guess work.”
YK

Yvonne K.

Admin. Assistant

Billing and Invoicing key features coverage

QuickBooks Enterprise offers 5 out of the 6 key features for Billing and Invoicing software identified by reviewers:

Invoice Processing
Invoice Creation4.6
Online Invoicing4.6
Invoice History4.7
Payment Processing4.5
Tax Calculation4.5

Pros and cons based on 20,610 verified reviews

61% of users rated QuickBooks Enterprise 5 out of 5 stars, while 2% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 20,610 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Comprehensive expense tracking

Ideal for small businesses

Effective financial management

Streamlined bookkeeping

Efficient tax management

Cons:

Frequent issue resolution challenges

Slow performance speed

Disruptive software updates

High cost concerns

Unreliable customer service

See pros and cons details

Pricing

Starting price:$2210 flat rate/per year|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

QuickBooks Desktop logo
4.4
(2.5K)

User insights about the payroll management feature

Reviewers feel that QuickBooks Desktop offers efficient payroll management by automating calculations, tax deductions, and paycheck generation. They appreciate the ease of processing payroll, direct deposit options, and the ability to manage employee profiles and payroll schedules. Users highlight the seamless integration with third-party time tracking vendors and the convenience of generating payroll reports. Some concerns include the cost and occasional support issues, but overall, they find it reliable and time-saving.
“I love the payroll management. You tell QB the individual hours and it processes checks for you. You can either do a check or have it direct deposited into employee accounts. I always use the "Enter Time" for the hours and that part integrates very well with 3rd party vendors for time tracking.”
BS

Beverly S.

Bookkeeper / Secretary

“I like the accuracy and efficiency that comes with this feature. This streamlines the complex process of calculating taxes, salaries and deductions, which saves me time and reduces likelihood of errors.”
SM

Shelmith M.

Admin Virtual Assistant

Billing and Invoicing key features coverage

QuickBooks Desktop offers 6 out of the 6 key features for Billing and Invoicing software identified by reviewers:

Invoice Processing4.6
Invoice Creation4.7
Online Invoicing4.5
Invoice History4.7
Payment Processing4.4
Tax Calculation2.0

Pros and cons based on 2,547 verified reviews

56% of users rated QuickBooks Desktop 5 out of 5 stars, while 3% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 2,547 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Comprehensive expense tracking

Ideal for small businesses

Efficient bookkeeping

Accessible learning resources

Robust accounting software

Cons:

Frequent and costly upgrades

Inefficient phone support

Challenging file management

Inadequate support

High costs and fees

See pros and cons details

Pricing

Starting price:$1922 flat rate/per year|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

QuickBooks Online logo
4.3
(8.3K)

User insights about the payroll management feature

Users report that QuickBooks Online makes payroll management easy and efficient, with features like automated tax calculations, direct deposit, and comprehensive reporting. They appreciate the integration with time tracking software and the ability to manage payroll taxes and employee data seamlessly. Reviewers highlight the user-friendly interface and the convenience of automating payroll processes. Some users mention occasional issues with customer support and the need for additional payroll options, but overall, they find it valuable for small businesses.
“By managing payroll through QBO, businesses can streamline the entire payroll process, ensure timely payments, stay compliant with tax obligations, and maintain accurate employee records. This leads to better efficiency and fewer payroll headaches.”
MW

Meagan W.

Manager

“If you use Quickbooks Online Payroll, taxes and return filing is automated. Email reminders to submit payroll. If you use QuickBooks Time (formally TSheets), approving timesheets is a breeze and imports into payroll to reduce double entry.”
NS

Nicole S.

owner

Billing and Invoicing key features coverage

QuickBooks Online offers 6 out of the 6 key features for Billing and Invoicing software identified by reviewers:

Invoice Processing4.4
Invoice Creation4.5
Online Invoicing4.5
Invoice History4.5
Payment Processing4.3
Tax Calculation4.3

Pros and cons based on 8,385 verified reviews

57% of users rated QuickBooks Online 5 out of 5 stars, while 5% gave it 1 or 2 stars. To determine these pros and cons insights we analyzed 8,385 reviews and identified the topics where users expressed positive and negative sentiment.

Pros:

Cloud-based accessibility

Ideal for small businesses

Seamless integrations

Comprehensive accounting features

Efficient tax management

Cons:

Frequent bugs and crashes

Limited desktop features

Recurring costs and price increases

Inadequate customer support

Complicated transaction management

See pros and cons details

Pricing

Starting price:$38 flat rate/per month|Free version:Not available|Free trial:Available

Prices may vary depending on the number of users and features.

Other Top Rated Billing and Invoicing Software with Payroll Management in 2026

QuickBooks Enterprise logo

Enterprise accounting, FSM and inventory management solution

QuickBooks Desktop Enterprise is an accounting software for small businesses which provides users with real-time access to customer, employee, and vendor information. The software includes tools for managing inventory, shipping, sales orders, pricing, tasks, invoicing, reporting, and more.

Read more about QuickBooks Enterprise

Users also considered
Rippling logo

Workforce management across HR, finance, and IT. 

Rippling Spend: Consolidate your business’s corp cards, bill pay, travel and expense management, into one modern system with built-in approvals, custom policies, and automatic reconciliation.

Read more about Rippling

Users also considered
QuickBooks Online logo

Accounting and business management software

Use QuickBooks Online to create custom invoices with your own branding. Insert Pay Now links to your invoices and accept payment via credit card or bank payment

Read more about QuickBooks Online

Users also considered
FreshBooks logo

Invoice and accounting software tailored to small businesses

FreshBooks lets you create, send & track invoices, as well as create expenses, send late payment reminders and account statements, and set up recurring billing.

Read more about FreshBooks

Users also considered
Dynamics 365 logo

ERP and CRM applications from Microsoft

Microsoft Dynamics 365 is a multi-language, multi-currency enterprise resource planning (ERP) software. The solution is designed for midsize and larger companies, and is fully customizable and extensible through its rich development platform and tools.

Read more about Dynamics 365

Users also considered
Xero logo

Cloud-based accounting software for small businesses

Xero is an award-winning online accounting software with billing and invoicing solutions designed for small business owners and accountants, available on any computer or mobile device with an internet connection. Easily manage your cash flow, bills, and invoices all in one place.

Read more about Xero

Users also considered
QuickBooks Desktop logo

Comprehensive business management solution

QuickBooks Desktop provides a comprehensive business management solution that integrates accounting, payroll, inventory, and multiple company management functionalities. The software offers industry-specific editions tailored for manufacturing, wholesale, contractors, and accountants, with features like advanced reporting, job costing, and automated pricing rules. Users can enhance their experience with cloud hosting capabilities that enable remote access and team collaboration.

Read more about QuickBooks Desktop

Users also considered
Hubstaff logo

Centralized app for time tracking and productivity metrics

Streamline your billing with Hubstaff: automate and track invoicing and billable hours seamlessly. Enhance your brand with customizable invoices. Easy integration with QuickBooks, PayPal, and more. No credit card needed, available for iOS and Android. Simplify billing in a few clicks.

Read more about Hubstaff

Users also considered
Jobber logo

Tool that manages quotes, schedules, invoices and tasks

Join over 250,000 home service pros using Jobber. We make it easy to schedule appointments, quote, invoice, and get paid faster. Organize your field service business and impress your clients - get started today.

Read more about Jobber

Users also considered
Wave logo

Accounting, invoicing, and payroll management platform

With Wave's comprehensive, free and unlimited invoicing tools, you can send invoices, keep track of who owes what, send reminders and more.

Read more about Wave

Users also considered
Timesheets.com logo

Time tracking, payroll, and billing for businesses

Timesheets.com tracks time and expenses to produce reports and exports to software like QuickBooks for invoicing.

Read more about Timesheets.com

Users also considered
Marketing 360 logo

Marketing Platform For Small Business

Send invoices with ease
Create and send online invoices and estimates in minutes. Get paid in one click 24/7 from any device. Keep track of the status of all your invoices in real time from one place.

Read more about Marketing 360

Users also considered
NetSuite logo

AI-powered cloud-based business management suite

Optimize receivables and accelerate cash flow by automating billing and invoicing processes with NetSuite's AI-fueled cloud accounting software. Transactions are posted to the GL automatically, which saves time, helps avoid error-prone manual data entry and ensures AR data is always up to date.

Read more about NetSuite

Users also considered
QuickBooks Online Advanced logo

Accounting & business management for small businesses

Automate billing and invoicing with customizable templates, batch processing, and real-time payment tracking for efficient operations.

Read more about QuickBooks Online Advanced

Users also considered
TimeCamp logo

A 100% free time tracker for teams. Unlimited users for $0.

TimeCamp is a time tracking platform with which SMBs can track billable hours, generate automatic invoices & manage employee time & attendance

Read more about TimeCamp

Users also considered
BigTime logo

AI-powered scoping, project, time, and billing software

BigTime helps reduce operational costs, align talent to projects, accelerate payments, and enable decision-making. With 20+ years of experience, BigTime can get you up and running quickly, operate with flexibility and agility, and enable you to solve today’s challenges and scale with you tomorrow.

Read more about BigTime

Users also considered
Odoo logo

All-in-one open-source business software

Easily manage recurring billing, subscribers, sales, and more with Odoo’s automated tools. Quickly provide clear contracts and flawless, automated invoices; take care of taxes without stress; and handle payments - all done automatically according to your settings.

Read more about Odoo

Users also considered
Everhour logo
Category Leaders

Time tracking, scheduling, budgeting & expenses software.

Everhour is a time tracker that can facilitate the billing & invoicing process and integrate with the most popular accounting software such as QuickBooks, Xero, and FreshBooks. Сhoose a billing method, set a billing rate, automate your invoicing process, and keep track of your finances fully.

Read more about Everhour

Users also considered
Patriot Accounting logo

Cloud-based accounting and payroll software

Patriot Accounting is an online accounting solution that allows businesses to track and manage transactions, import bank transactions, reconcile accounts, send estimates & invoices & more.

Read more about Patriot Accounting

Users also considered
Agiled logo

Software for managing business operations

Agiled is a cloud-based business management software designed to help businesses of all sizes manage invoicing, contracts, employees, finances, and other operations on a unified portal. Its project management capabilities allow organizations to handle tasks, project details, and team members using customizable templates, view, edit and share schedules with clients using Gantt Charts and create and assign tasks to teams.

Read more about Agiled

Users also considered
Replicon Time Tracking logo

Cloud-based project time tracking platform

Replicon Time is a leading cloud-based project time tracking platform that helps mid-market and enterprise organizations manage time, projects, and workforce operations with accuracy and confidence.

Read more about Replicon Time Tracking

Users also considered
FieldPulse logo

Cloud-based field service management software

FieldPulse is a cloud-based field service management software designed for service contractors that helps manage business operations and workflows, including customer management, scheduling, project management, estimates and invoices, timesheets, customer portals, and more.

Read more about FieldPulse

Users also considered
ActiveCollab logo

A productivity and collaboration workspace for teams

In ActiveCollab, you can create and send out custom invoices, including eInvoices, link them to your QuickBooks account, and analyze for insights into your pricing, client payment behavior, and more.

Read more about ActiveCollab

Users also considered
Holded logo

ERP, Accounting, Invoicing & more for freelancers and SMBs.

It's a cloud-based invoicing software for freelancers, SMBs and accountant offices to control all aspects of their business and optimise their management.

Read more about Holded

Users also considered
Sage Intacct logo

Best-in-class Cloud ERP for Finance

Ensure your purchasing team is able to place the right orders at the right time for the right price with Sage Intacct

Read more about Sage Intacct

Users also considered

Key features for Billing and Invoicing software

Based on GetApp's analysis of verified user reviews collected between July 2021 and August 2024.

  • Invoice Processing: Users highlight the ease of storing, reviewing, and managing invoices, integrating OCR for data extraction, and automating payment tracking and approvals. 95% of reviewers rated this feature as important or highly important.
  • Invoice Creation: Reviewers value the customization options, template availability, and the ability to quickly generate professional invoices tailored to business needs. 94% of reviewers rated this feature as important or highly important.
  • Online Invoicing: Users appreciate the convenience of sending and tracking invoices online, integrating with payment systems, and customizing templates for branding. 92% of reviewers rated this feature as important or highly important.
  • Invoice History: Reviewers emphasize the importance of tracking previous invoices, payment statuses, and customer details for easy reference and financial management. 91% of reviewers rated this feature as important or highly important.
  • Payment Processing: Users find the integration with various payment methods convenient, ensuring secure transactions, tracking, and managing payments efficiently. 91% of reviewers rated this feature as important or highly important.
  • Tax Calculation: Reviewers mention the automated tax calculation based on location, compliance with tax laws, and the ability to include taxes directly in invoices. 82% of reviewers rated this feature as important or highly important.