14 Best Apps to Pay 1099 Independent Contractors and Freelancers

16 May, 2022
Wayne Richard

Wayne Richard

9 minutes
best applications

If you are like most eCommerce businesses, you’ve probably hired at least a handful of freelancers to help you with specific tasks in your business. 

However, navigating how to pay both employees and 1099 contractors in the U.S. or international freelancers without incurring  exorbitant fees can be a time-consuming and frustrating experience. 

You also need to take into account business payroll processes, different currencies, FX spread, retirement plans and benefits (for full-time employees), and how it integrates with your accounting software. 

Fortunately, there are many online payroll software solutions designed for small to mid-sized businesses. There also are online solutions to help you pay international freelancers and vendors. 

In this post, we’re sharing 14 online payroll solutions designed to take the headache out of paying employees, 1099 contractors, and international freelancers. 

1. Airwallex 


Airwallex is a business bank account designed for modern online businesses. In addition to opening global accounts and borderless cards, you can also send payments to freelancers and vendors in 23 currencies at market-beating rates. So, you’ll be able to spend less money in fees. 

They have different pricing options depending on your needs from business accounts to platform (which also includes international transfers).  

2. Wise 


Wise (formerly called Transferwise) is a money transfer service used by over 10 million people worldwide. Launched in 2011, Wise is a safe and efficient way to pay for services from the US to over 80 countries using your phone or app. Wise uses the real exchange rate and charges low transfer fees, which can save your business money. You can transfer funds using your bank account or credit card. 

You can pay overseas invoices that are one-time, recurring payments, and mass payouts. The fee gets cheaper if you send amounts above 100,000 GBP either as a single transfer or with multiple transfers in a month. The batch tool allows you to send up to 1,000 payments in one transfer. You can fund a transfer using a bank account or credit card. Payments arrive quickly, with about 50 percent received instantly or within an hour. 

wise pricing

You can create a Wise business account for free, or you can set up an account that allows you a banking alternative for a fee. The banking alternative lets you receive payments from a third party, establish an IBAN, sort code, and more.

wise pricing plans

3. Gusto


Gusto is a full-service, all-in-one platform for cloud-based payroll, benefits, and human resource management software. Launched in 2012 as ZenPayroll, Gusto now services more than 100,000 businesses in the United States.  

Gusto’s software makes it easy to process your payroll in minutes. You can pay contractors or employees. It syncs your team’s hours automatically and summarizes your payroll for easy review. This platform also calculates and files your taxes with the correct government agencies every time you run payroll.

Gusto has several different plans to suit your business’s needs. The contractor plan starts at $6 per month per person for companies that only have 1099 contractors. 

gusto pricing

4. PayPal


Established in 1998 as Confinity, PayPal is now a leading online payment system. PayPal is a secure payment method since it keeps your personal bank account separate from the transaction. To pay another PayPal user, you transfer the funds from your bank account to your PayPal account and then process the transaction. 

You can use PayPal for your 1099 contractors, but you and your contractor will need a PayPal business account. You can’t use the “friends and family” option when paying for a service that was performed. PayPal will automatically produce a 1099-K form at the end of the year. This function saves you from having to send a 1099-NEC form. 

You can use it in over 200 countries. That said, if you make frequent or large international contractor payments, you may want to use other systems like Xoom (owned by PayPal) or Wise for more cost-effective currency exchange options. 

You can set up a PayPal business account for free in a few minutes. You’ll need to provide your business email address and basic information about your business. You’ll then be able to pay invoices, send money, and more through your company. There is a PayPal enterprise option that can help businesses streamline operations and accelerate growth, but no pricing is available on the website.

paypal pricing

5. Zenefits


Zenefits is a cloud-based human resource information management platform for small to mid-sized businesses. Founded in 2013, this platform helps companies manage their payroll, benefits, health insurance, taxes, and more. 

You can pay employees and independent contractors through Zenefits Payroll. When working with contractors, you can opt to have Zenefits generate 1099s. You also can add contractors to your regular pay runs if preferred or pay them through an off-cycle run. This tool helps save you time when running payroll and to stay compliant with taxes. 

Zenefits pricing

Zenefits offers three different plans to suit various businesses’ needs, plus an enterprise plan for larger companies. Prices start at $8 per employee for the annual plan or $10 per employee for the monthly plan. They also offer a free 14-day trial.

6. Justworks


Justworks helps you manage payroll, HR, compliance, and benefits. Founded in 2012, Justworks makes it easy to automate and run payroll, including managing benefits, deductions, and taxes. 

You can pay employees or independent contractors using automatic direct deposit payroll. You also can pay vendors. Other features include setting up payment reminders, splitting deposits across multiple accounts, one-off payments, payroll tax filings, and more.

justworks pricing

Justworks offers a Basic plan and a Plus plan. The price of each plan varies depending on the business’s number of employees. The Basic plan is for companies with less than 25 employees and starts at $49 per month per employee. 

7. Bill.com


Bill.com is a cloud-based payments platform for small to medium-sized businesses. This platform helps companies manage their accounts receivable, accounts payable, or both functions. Founded in 2006, Bill.com supports fast and secure ACH payments and automates approvals, saving businesses time. 

This program allows you to schedule payments to vendors, lets customers auto-pay your invoices, or set up auto-reminders. Bill.com provides a flat fee for ACH transactions instead of a percentage rate fee, so you always know the exact fee. You can use Bill.com to pay independent contractors and employees. 

bill pricing

Bill.com offers four different pricing plans to fit any business’s needs. Plans start at $39 per user per month. 

8. OFX


OFX helps small to mid-sized businesses transfer money internationally to pay overseas suppliers, staff, contractors, and make transfers to your overseas accounts. Founded in 1998, it allows businesses to transfer money to over 190 countries in 55 different currencies.

OFX makes it easy to get started. Companies can set up an account in minutes and be able to start transferring money immediately. You can send money through ACH direct deposit or wire transfer. Most transfers take between 1 to 2 business days. You can track transfers online or through their app. 

ofx pricing

OFX does not currently charge a transfer fee for international money transfers. The company does note that some third-party banks may deduct a fee, but that does not go to OFX. You can check rates on your global money transfers on OFX’s website. To calculate your OFX customer rate, you need to first log in. 

9. Paychex Flex for Small Businesses


Paychex Flex for small businesses provides payroll services for companies with up to 49 employees. Started in 1971, this platform lets you run payroll online from a desktop or mobile device, has automatic payroll tax administration, online employee self-service, and more.

This software makes it easy to pay various workers, including 1099 contractors, salaried employees, and hourly employees. You can pay using direct deposit or pay cards. You also can pay with paper checks, although an additional fee may be added depending on your plan. All plans include complete payroll tax administration and new-hire reporting.

paychex pricing

Paychex offers three payroll packages starting at $59 per month plus $4 per employee for the Paychex Go plan. Prices are not listed for the other plans. You’ll need to contact Paychex for a quote.

10. Patriot Payroll

patriot payroll

Patriot provides online payroll software for small to mid-sized businesses with up to 100 employees. Founded in 1986, Patriot makes it easy to run payroll. You enter employees’ work hours and contractor payments. The software runs payroll, and then you review and approve. You can pay employees and contractors with free direct deposit or print paychecks or pay stubs using your printer.   

patriot payroll pricing

Patriot offers two service plans: Basic and Full Service. The basic plan starts at $10 per month plus +$4 per employee or contractor, while the Full Service plan starts at $30 per month plus $4 per employee or contractor. In the Full Service plan, Patriot will manage your payroll taxes, including filing federal, state, and local taxes plus year-end taxes. Patriot also offers a 30-day free trial offer. 

11. Square Payroll

square payroll

Square Payroll is an all-in-one payroll system with automated tax filings designed for small businesses. Started in 2015, it is available in all 50 US states plus DC. The software helps companies run payroll, manage employee benefits, and automatically file payroll taxes, which saves businesses time. 

pricing for square

Square Payroll makes it easy to pay employees and contractors with its flat pricing and cancellation anytime policy. One plan is specifically for businesses that only use contractors. You pay a $5 monthly fee per person paid for the contractor only plan. The plan allows for free seasonal inactivity, mails all 1099-MISC forms, and offers pay by check, direct deposit, or Cash App. 

Square Payroll offers a plan with a $29 monthly subscription fee plus a $5 monthly fee per person paid for companies that have employees and contractors. This plan provides full-service payroll, automatic payroll tax calculations, live support, and more. 

12. Melio


You can use Melio to pay invoices from contractors and vendors. Unlike some of the other options, it is free to use for bank / ACH payments. You only pay a transaction fee for credit card payments. They have payment approval workflows and work with all of the major credit card companies. 

Unlike some of the other software options, Melio doesn’t have any monthly plans. Instead, their pricing is transactional meaning you only pay when you use it for sending and receiving credit card payments.  

13. Deel 


Deel makes it easy to hire, work with, and pay talented people all over the world. They automate the most tedious parts of hiring, onboarding, and payroll compliance. So, you can focus on growing your team and not have to worry about knowing the ins and outs of the laws and regulations of every country you are hiring in. 

Another advantage to using Deel is they make it easy to pay contractors and employees via the most popular cryptocurrencies like bitcoin and ethereum. 

Pricing starts at $49 per month per contractor or $599 per month per employee. 

14. Paytron 


Similar to Airwallex, Paytron is solving the problem of needing to have multiple different banking apps. They do FX, virtual cards, accounts payable processing that can load directly to the bank (like Bill.com), and direct debit. 

While this business is new, it is already capturing significant market share of Australian small businesses.  

They offer a 30 day free trial, and business plans start at $49 per month AUD. 

As a business owner, you have options when it comes to business payroll software and how you pay employees and contractors. When reviewing available platforms, you may want to consider whether you need a platform that supports international services, offers payment methods you prefer and whether you need tax assistance.

Whether you are looking for bookkeeping support, help with payroll compliance, or need to clean up your Xero account, we can help. Schedule a free call with a Bean Ninjas team member today.

Posted By

Wayne Richard

Wayne Richard

Wayne is a management accountant who forged a 15-year career with tech heavyweight Hewlett Packard before starting his own cloud accounting firm in Tucson, Arizona. Fate (and the Internet) brought him to discover Bean Ninjas via a blog post. Two years later and Wayne’s involvement with Bean Ninjas had grown from a blog comment to contractor to equity partner. When Wayne isn’t managing a global team and equipping entrepreneurs with the financial tools they need to enjoy business success and lifestyle freedom, he’s being an everyday superhero to his wife and five children. Wayne is Bean Ninjas resident e-commerce expert.

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