Best Invoicing Software: Freshbooks vs. Paypal & More

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Last updated on March 9th, 2019 at 07:42 am

best invoicing softwareInvoicing can be such a chore, and many people don’t enjoy doing it.  The problem is that as a small business, you have to.

Thankfully for all of us, there is plenty of invoicing software out there to make it a lot easier.

We took the time, did the research and outlined the various features of the best invoicing options available for you.

From Freshbooks, Netsuite, MHelpDesk, Billquick, PayPal, Unanet, Anytime Collect, Invoiceocean, Invoicera, Paper Free Billing and even Invoice Expert, the list to choose from is endless.

What Features Do You Need From Your Invoicing Software?

Different Invoicing Options

How do you go about choosing the best invoicing method to cater to all your needs?

Do you need an online payment option, recurring invoices, files attached to invoices, financial reports, time tracking, auto-billing, multi-currency, or even automatic receipts?

The list is endless but don’t fret; the criteria below should quickly help you make up your mind.

Merchant Services

Online platforms such as Square and Paypal allow you to send invoices, including links for payment via credit cards by customers.

They are both free, and if online payment appeals to you and your business, these options would be ideal.

One should, however, note that with each payment transaction, approximately 3% goes to transaction fees.

Full Accounting Systems

These not only offer invoice services, but they also provide integrated accounting and payroll services. Examples of these are Zoho Books and FreeAgent.

Why We Recommend These Companies

Different software platforms offer different invoicing features, all of which are advantageous to a small business.

Below we will discuss the best invoicing software, top of our list being Freshbooks, MHelpDesk and Paypal.
After extensive researched, we settled on the following providers, as they outperformed the competition:

Our Pick for Best Invoicing Software: Freshbooks

We strongly recommend Freshbooks as the best invoicing software due to its friendly user interface, super-packed features, highly rated customer service and the fact it comes in at an affordable price that suits almost any small business.

1. Freshbooks

Best Invoicing SoftwareBased in Canada, Freshbooks is cloud-based invoicing software that has served over 5million customers globally since 2003.

It offers time tracking, expense/revenue tracking (that can be exported to QuickBooks) and invoicing services for small businesses.

Additionally, it also provides multiple payment processing options. The software works best for small businesses comprised of small teams or self-employed workers.

Freshbooks also allows invoices to be sent via physical mail and is multicurrency in nature.

Features and Integrations

Freshbooks offers features such as time tracking, expense/revenue tracking, payment processing, estimates, recurring invoices, auto-payment and it is multi-currency.

Additionally, the software saves a list of services/products and can be used to send invoices via physical mail. Another advantageous feature in Freshbooks is that it can apply sales tax separately to each item on the invoice.

Some of the integration features on Freshbooks include accounting using Quickbooks, CRM (Capsule and BatchBook), eCommerce via Shopify and zen cart, payment processing through approximately 13 platforms such as PayPal and Stripe.

Digital signature by Right Signature,  Mailchimp, project management using Basecamp Classic and Zapier. Other integrations are POS by Shopify and help desk through Freshdesk and Zendesk.


Freshbooks offers three different pricing plans suited to serve different customers.  The Seedling plan provides basic invoicing features at $20 a month for one user invoicing up to 25 customers.

The Evergreen plan costs $30 a month and serves two users and allows invoicing for an unlimited number of clients.

It also avails access to team expense reporting and their timesheets. The Mighty Oak plan at $40 a month offers similar features to the Evergreen plan but allows up to five additional users on one’s account.


This invoicing software is easy to use allowing an easy set-up.  It is also easy to navigate with no bugs or button response issues. Freshbooks offers excellent client support using both phone and email.

It also avails user guides, tutorial videos and searchable FAQs on its web page support centre. Additionally, Freshbooks is available as a mobile app using iOS and Android formats.

With Freshbooks, you can apply sales tax to each item on the invoice and offers up to two tax fields for each item.

This works best if some of your items are taxable while others are not. Payment processing is efficiently conducted since there is a link for clients to directly pay on the invoice via credit card.

One can also use external payment processing services such as those from PayPal,, Stripe and others.

Additionally, transaction fees are automatically imported in the form of expenses and clients can be auto-billed at no extra charge.


Freshbooks is not suitable for big businesses that need accrual based accounting despite its name portraying it as “true” accounting software.

It also does not work well for small businesses looking for a basic invoicing platform.

Additionally, while applying sales tax, tax rates cannot be imported based on a client’s location.

With Freshbooks, one cannot customize invoice formatting to allow for placement of field titles and object on the invoice.

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2. mHelpDesk

With over 12,000 clients, mHelpDesk is a work order, job tracking and invoicing software suitable for field-based businesses (those that work offsite).

That need to bill clients on the spot or organize appointments such as caterers, repair services, and event planners, among others.

The software allows for easy management of employee schedules and makes it easy to monitor their locations wherever work has taken them.

Employees, on the other hand, can track time using mobile devices, have clients sign off on it using mHelpDesk’s digital signature tool, pay via credit card and create an invoice/estimate.

mHelpDesk software is multicurrency and offers a 14 day free product trial. It is similar to Connect2Field, and the company is based in the USA.

Features and Integrations

mHelpDesk comes with time tracking, estimates, payment processing, customized invoice formatting, recurring invoices, multicurrency platform and a save list of products/services.

The software has QuickBooks (accounting) integration only and allows you to apply sales tax that has to be however saved beforehand under “Settings” > “Sales Tax Items.” When creating the invoice, you will have to specify which items are taxable or not.

You also have to determine which tax rate you are using at the bottom of the page, and one can only apply one rate to the invoice.

Pricing Plans

mHelpDesk offers three price packages. The Pro Package serves one user with invoicing features at $95. Any additional users are charged at $25 a month each.

The Business package is available at $149 per month for up to five users. Any additional users are charged at $20 a month each.

The Enterprise Package is for an unlimited number of users, but you have to call the company for pricing.


mHelpDesk is easy to use allowing an easily guided set-up process. This invoicing software has a very reliable and knowledgeable support team, available via phone and email, as attested to by different users.

It also offers user guides, tutorial videos and FAQs on its web page support center.


mHelpDesk is more pricey compared to most of its competitors such as Freshbooks, but the location features account for the extra cost.

It also has limited third-party integrations to support its services and takes some time getting used to. It is also not as fast as the other invoicing software, but it gets the work done.

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3. PayPal

PayPal is a free, easy to use, online, multicurrency payment processing and invoicing platform for businesses interested in quickly setting up and are not in need of tools such as recurring invoices, auto-billing or time tracking.

The online platform is not the most professional looking but offers features such as a list of products/services, taxes, discount and due date.

With over 160million active users globally, its invoicing software is similar to Square Invoice. Being also an online payment platform, it removes the need for multiple accounts.

The transaction fees charged at almost 3% per transaction are however pricey. It is, however, cheaper compared to its competitors. The platform is cloud-based.

Features and Integrations

At a fee, PayPal invoicing offers a save list of products and services, payment processing, customized invoice formatting and is multicurrency.

Its integrated features include accounting using Quickbooks, Xero, Wave and Zoho Books. Time tracking is also available using Harvest while Shopify and Big Commerce serve as the eCommerce integrations.

Payment processing can be done via PayPal itself or using Stripe and Zapier comes on board for project management. Also available is POS using Shopify and Vend platforms.


PayPal Business is free to use although to get additional features you have to upgrade, which calls for payment. The upgrade offers two pricing packages.

Paypal Payments Advanced is available at the cost of $5 a month and has the same features as the free account. It, however, allows one to process payments directly to one’s website by integrating the two.

PayPal Payments Pro, on the other hand, is available at $30 a month allowing you to host your checkout page, allowing customization and more control. One can also accept credit cards using either phone or mail.


Setting up PayPal, despite not having a guided format, is relatively simple. Given that it is both an invoicing and payment processing platform, this negates the need for another account to accept payments.

Additionally, to link your bank account to the site, all you need are your account and routing numbers. The free business account option with PayPal is pretty straightforward allowing you to send money, view transactions and invoice customers.

Additionally, PayPal support services are available via phone and email. FAQs and articles on using the site are also available on the web-based help center.

Depending on the user, the support team is both knowledgeable and reliable.

Using Zapier, Zoho CRM, Insightly, Salesforce, Nimble, Basecamp, Base CRM, Freshdesk and Trello are available by syncing data between PayPal and these platforms.

Additionally, clicking on the payment “request” option saves time given that it is essentially a simplified invoice where you just type the recipient's email and amount of payment.

PayPal allows tax application to each separate item which is ideal when not all your products/services are taxable using a pre-saved tax, or by entering a new one on-the-fly.


With the free business account, an older user interface is used and clicking on the icon “Merchant Services” is slightly confusing since this move switches you to a separate menu.

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Best Invoicing Software for Small Business: Other Alternatives

All businesses should find invoicing services that suit and meet all their needs. The three platforms Freshbooks, mHelpDesk and PayPal do not suffice all the time.  The software below offer viable alternatives in such cases:

1. Square Invoice

Like PayPal, Square is a free credit processing merchant service with an invoicing system suitable for when one has many small orders.

According to Javelin Strategy & Research, Square has a market share of between $100,000-$1 million in annual sales of small businesses.

Features and Integrations

Payment processing and save list services/products are the main features on Square while accounting and eCommerce are what make up its integrations.

For accounting, Quickbooks, Zoho Books and Xero are available while Big Commerce and Weebly support its eCommerce services.


For every payment transaction using Square, a flat fee rate of 2.75% of the transaction value for invoices and swiped credit cards and 3.5% + 15 cents for manually entered credit cards, is charged.


The cloud-based Square software located in the USA is free to use with all its features and offers free credit card swiper service.

The invoicing software is easy to set up and comes with free card reader once you type in your shipping address and bank account and routing numbers for receipt of payment. Invoicing services are also cheaper when compared to those on PayPal.

Square has straight forward menu pages which allow you to view dashboards for sales, customers, employees, appointments and more.

It also offers support service on Twitter and via phone or email. Articles on the invoicing software together with user guides are available on its web page.

The sales tax application service is available with Square by saving rates beforehand under the “Items” menu.


Unlike PayPal, one has to confirm his/her identity using one’s SSN.  This can, however, be time-consuming if your home address is different from that on your SSN file.

Phone support services come with lengthy wait times, which have witnessed complaints from many clients.

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2. Chargify

Chargify is an invoicing software suitable for small businesses that use subscription billing for their products and services such as publications and cleaning services.

As of March 2015, a total of close to 1500 businesses were using the platform. Similar to Zuoro and Zoho, Chargify recurrently bills clients and sends them invoices automatically.

It also provides the option of creating an order page for customers to sign up for you products and services.  This allows you to manage such subscriptions easily.

Features and Integrations

Recurring invoices, payment processing, multicurrency, customized invoice formatting, auto-payment, and save lists for products and services form its core features.

To support service provision, Chargify has integrations such as Zapier, CRM (Salesforce), Shopify for eCommerce, Xero for accounting and Clickdesk acting as the HelpDesk. Lastly, Stripe and serve as its payment processing platforms.


This comes in four categories.  The New Idea level costs $65 a month for basic billing features, API Access and the option of creating a customer self-service portal for up to 20 customers.

Any customers above this number cost +$2 per month.  This level also offers phone support.  The Small Businesses level is available at $129 a month for up to 500cutomers.  Above this, the billing rate is +$1 per month.

One also gets access to the tech support line unlike at the New Idea level.  The Small Business Plus level is similar to the Small Businesses level and costs $169 a month.

Additionally, it integrates support features such as MailChimp, Xero and Salesforce.  The Growing Businesses level supports up to two thousand customers and costs $459 a month.

Any customers above the 2000 mark are charged at +$0.69 dollars per month. At this level, priority customer support is also at your service.


As invoicing software, Chargify avails multicurrency use and offers a free trial period.  It also has 24/7 support phone services and a very knowledgeable and reliable response team.

The platform has a sophisticated sales tax application system that incorporates different taxes and tax rates for different countries.  There is also a Chargify mobile app for iOS devices.


Chargify does not offer time tracking, sending of invoices via physical mail and it costs more compared to most of its competitors.

Unlike other invoicing software, Chargify takes more time to set up and can be a tad confusing thanks to some of the terminology used and difficulty in locating the correct menu pages.

Unfortunately, the platform does not provide adequate video user guides to ease this process.

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3. Zoho Invoice

Zoho Invoice is custom branding invoicing software that can be purchased alone or together with Zoho books.

With over 13million users of all their products, this invoicing software is similar to Freshbooks and Harvest.

Features and Integrations

Time tracking, estimates, save a list of products and services, payment processing, customized invoice formatting, recurring invoices and multicurrency comprise its key features.

Zapier, Zoho Projects (time tracking and project management), Zoho CRM (CRM), and payment processing using Stripe, Paypal and cater for its integrations.


Zoho Invoice provides two pricing options: free or paid.  The free option is for one user invoicing up to five different customers.

The paid option comes in two forms, the Standard Edition which costs $15 per month for three users and up to 500customers and the Professional Edition at $30 a month for an unlimited number of customers and users.


Zoho Invoice is suitable for those looking for professional looking customizable invoicing templates.  It also allows for invoices to be sent via physical mail, supports multicurrency use, offers time tracking services and a free trial period.

Additionally, it is cheaper compared to most of its competitors.  The set up for Zoho Invoice is straight forward and easy to use.

The software also offers phone and email support services for 24hors, five days a week.  One can also apply pre-saved sales tax rates for each item.


Zoho Invoice does not offer accounting tools, and one cannot accept/decline estimates with a single click.

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4. Wave

With over 2.5million users, Wave is an invoicing, payroll and accounting software for small businesses that want free accounting tools.

Features and Integrations

Multicurrency, auto-import bank statements, payment processing and five types of accounts are the features of this invoicing software.  For integrations, it has Etsy, Shoeboxed for receipt scanning and payment processing.


A full featured version of Wave is available for free, and payment systems only kick in when one has to use payroll or premium customer support features.  For payroll, charges are $15 per month and $4 per employee.

Above ten employees, the price drops to $1 per person. For $9 a month, access to live chat support between 9am-5pm EST is available for the plus package.

The Advanced package costs $19 a month and incorporates phone support during business working hours.


Wave is suitable for start-ups and self-employed people who see no need of outsourcing accounting services and do not need advanced systems such as Xero and Quickbooks.

It offers free trial period and is cheaper compared to other invoicing software.


The software offers only Stripe as a payment processing platform and provides very little automation for accounting features.

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Our Final Review for the Best Invoice Software

To conclude our review, the best invoicing software is Freshbooks, not only is it affordable for most small businesses, but it is also easy to use, has many useful features and offers top-notch customer service.

Using Freshbooks, you can easily create professional invoices and send them to your clients.

You can also accept online payment from platforms such as PayPal, have access to features such as time/expense tracking, recurring invoices, auto-billing (assists in managing subscription services) and even automatically.

Send invoices through the mail which is convenient for customers who don’t like paying via email.





The WiseSmallBusiness Team is full of industry experts and successful business owners  willing to contribute important business articles.


  1. I’ve used Freshbooks for my business for the past two years and love it. I looked at alternatives for better pricing, but I think I’m gonna stick with what I have. It’s better to pay a few more bucks and use a service you can rely on. Just my two cents!

  2. The Application is fabulous. I was able to get the invoice to export, which is great. The ability for it to “auto” link to a client versus manual selection each time would be very helpful on this. Also, choosing clients from QB when creating projects, and other cross functional things like that would really help. I also found some good review about mhelpdesk on this site too.

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