Shypyard Blog

Left stranded after OneSaas's shutdown?

Don't worry, Shypyard's got your back! Migrate today to ensure your workflows aren't out of sync for too long and take advantage of our free 14-day trial.

Start your Free Trial
Blog Posts

A Guide to PayPal for E-Commerce Merchants

Thanks! Your vote has been received and will be used to determine our upcoming blogs.
Submission failed, please try again

What You Need to Know

  • There are 3 main ways you can set up PayPal to receive payments. Additionally, PayPal's other services can help you manage the entire payment side of your business, from the checkout flow to security checks.
  • However, the monthly and transactional fees of the different aspects of PayPal can be complex and different for each country. As such, it helps to track your store's PayPal transactions separately to gain a better understanding of your monthly PayPal fees.
  • With Shypyard, you can integrate your PayPal transactions with your accounting system to simplify and automate data and transaction fee tracking.
Start your Free Trial

As a merchant selling or planning to sell products online, collecting payments from customers is extremely important, for many obvious reasons. Therefore, finding a suitable payment service provider—a third party to help you accept payments and handle transactions—is a crucial step in establishing, maintaining, and growing your business.

PayPal is undoubtedly one of the most famous choices for e-commerce merchants. Hundreds of millions of people already use PayPal to send and receive payments, and using it for your payment processing can increase the trustworthiness of your online store. However, what is PayPal like, what services does it provide, and is it right for you?

This blog will serve as an in-depth guide for e-commerce merchants who are looking into PayPal as the means to handle their payment transactions.

What is PayPal?

PayPal allows for fast, secure money transfers from one party to another. It is available in more than 200 countries and accepts 25 different currencies. Both businesses and individuals use it, which is why new users can choose to set up either a personal or business account.

PayPal lets merchants accept payments paid with debit cards, credit cards, PayPal accounts, Venmo, and other methods. E-commerce merchants can set up different payment pathways, ranging from simple or customized. They can create shareable payment links, send customized invoices that accept multiple online payment options, or add a whole checkout flow to their store.

PayPal is suitable for merchants who want a flexible, end-to-end, single-platform solution for processing payments. Its tools have been designed to be scalable, so PayPal can service growing businesses without hitches.

Ways to Accept Payments with PayPal Business

E-commerce Platform

If a merchant sells products on an e-commerce platform, like Shopify or BigCommerce, it is likely that PayPal is already a choosable payment provider option there. As a result, once the merchant creates a PayPal account, connecting it and their store is as easy as selecting it in the platform's settings. What is better, if the merchant connects multiple platforms or marketplaces to their PayPal account, they would be able to track all their transactions in one place.


In Shopify, a merchant is given a PayPal Express Checkout account immediately after they create a Shopify store. The account is set up with the same email they use to log in to their store. If they already have a PayPal business account linked to the same email, they can start receiving order payments with PayPal right away. If not, they can either add their Shopify email to their existing PayPal business account or sign up for a new account with the email.

In addition, from their PayPal account, the merchant can give Shopify permission to issue refunds and to allow manual payment capture using PayPal.

In PayPal's account settings, the merchant can also enable guest payment, which would let their Shopify customers pay using credit or debit cards even without a PayPal account. Otherwise, the default PayPal Express setting is to ask customers to log in or sign up to PayPal before proceeding with the payments.

To learn the steps of setting up PayPal in Shopify, visit Shopify's official help page.

Your Own E-commerce Website

If they sell products on their own website, e-commerce merchants can use PayPal Checkout to receive payments. PayPal Checkout can range in customizability, depending on the coding capabilities of its adapter.

  • Quick setup: At its simplest, PayPal Checkout can be set up in minutes. It can provide a simple payment button next to a product. People would simply click on the button to pay for a fixed number of a fixed product. To set it up, E-commerce merchants just need to complete a form and design the button's appearance on PayPal (see top picture). For example, they can add a brief product description, define the product price, and change the color of the button. Afterwards, the code for the customized button is automatically generated and just needs to be pasted next to the intended product. The whole setup process requires no coding on the merchant’s end. The resulting payment process is also a simple affair and even saves the store from needing to add a shopping cart before being able to receive payments.
  • Standard integration: Integration of PayPal Checkout and the product and payment page of their online store is more suitable for most e-commerce merchants. Shoppers will be able to see the different PayPal payment options upfront. This checkout experience will overall be more personalized and flexible than the payment button option. This integration is slightly more complex and uses the PayPal JavaScript SDK to present relevant payment options to buyers. An online merchants would need to copy and paste the sample JavaScript SDK code into the code of their checkout page. They would then have to modify it a little, although to what degree depends on their needs and capabilities.
  • Advanced Integration: For e-commerce businesses that require the services of the standard integration but also a fully customized layout and look, advanced integration is suggested. E-commerce merchants can even set up risk tolerant filters with PayPal’s fraud protection tools. However, relatively complex coding is required for advanced integration. As a result, a developer may be needed to handle the integrations.

Other Methods


PayPal allows e-commerce merchants to create an invoice that can be sent via email or a link. Business logos, contact information, colors, and other elements can all be added to the invoices as customizations. The invoice can even be set to be scheduled or recurring so that its delivery occurs automatically. Furthermore, PayPal provides e-commerce merchants with the ability to track billing status and send invoice payment reminders. Finally, if a PayPal estimate was already sent to a customer beforehand, it can be quickly transformed into an invoice if necessary.


An e-commerce merchant can create a PayPal.Me link in less than a minute and share it via any means to their customers. A customer just needs to follow the link and enter a money sum to pay.

Sell on Social

One can also use PayPal’s Sell on Social feature to instantaneously create a simple product page that can be easily shared via a link. People who open the link can click on its embedded “Buy Now” button to purchase the product for its fixed price.

Virtual terminal

Merchants who take orders over the phone can use PayPal’s virtual terminal to process debit and credit payments.

Other Features of PayPal Business

PayPal is more than just a way to collect payments, it also offers a multitude of other tools and back-end services. PayPal’s tools can help a business run reporting and analytics, streamline operations, manage disputes with customers, handle monetary transactions, protect from fraud, and more.

For example, on PayPal’s dashboard, e-commerce merchants can gain quick insight on their PayPal balance and invoices. They can also view records of their past transactions and apply filters to find transactions of a specific characteristic. Furthermore, they can learn about their store’s sales, checkout activity, customers, and disputes & chargebacks by leveraging PayPal’s in-depth analytics feature.

The various services of PayPal are put on display in the PayPal Merchant App Centre. These features can be pinned onto one’s PayPal dashboard for quicker access.


PayPal Standard

When a merchant first registers for a PayPal business account, there are no initial, hidden, monthly, or termination fees. This is PayPal Standard. PayPal in PayPal Standard handles every aspect of the payment process, from the checkout to security checks. Customers are transferred to PayPal's site to complete the procedures before they are sent back to the store. PayPal charges a transaction fee for each processed payment.

  • The transaction fee of PayPal payment option transactions is: 3.49% + $0.49 USD.
  • The transaction fee of credit and debit card transactions is: 2.59% + $0.49 USD.

PayPal Advanced

PayPal Payments Advanced is an advanced solution currently only available in the US and Canada. It provides e-commerce merchants with an embedded checkout form hosted on PayPal’s servers. In other words, to your customer, they appear to stay on your website during the checkout process; however, in reality, the payment is being processed by and sent to PayPal’s servers.

In addition to the per-transaction fees, PayPal Advanced has a monthly fee of $5 USD.

PayPal Pro

PayPal Payments Pro is an advanced solution currently accessible in the US, UK, and Canada. It allows e-commerce merchants to completely customize the checkout experience for their customers. They are able to host the checkout process on their own site and design it to match their branding. PayPal Pro also includes the Virtual Terminal function.

Besides the per-transaction fees, PayPal Pro has a monthly fee of $30 USD.

Individual Services

Think of PayPal Payments Advanced and Pro as bundled deals. Instead of paying for the whole package, one can also choose to only adopt a few particular additional features to better service their e-commerce store’s needs. These features have their own monthly and per-transaction fees. Just to list a few:

  • Invoicing has no monthly fee and a per-transaction fee of 3.49% + $0.49 USD.
  • Virtual Terminal as a standalone service has a monthly fee of $30 USD and a per-transaction fee of 3.09% + $0.49 USD.
  • Advanced Fraud Protection Services has a monthly fee of $10 USD and a per-transaction fee of $0.05 USD.
  • Buyer Authentication Service has a monthly fee of $10 USD and a per-transaction fee of $0.10 USD.

In addition, PayPal:

  • Applies a different transaction fee for micropayments
  • Adds an additional 1.5% to the per-transaction rates of international transactions
  • Has a 3-4% currency conversion fee

To learn more about PayPal pricings, visit: Make sure to confirm that the correct country is listed under the section “Relevant Market/Region”, as the pricings also differ based on the country your store is in.


As a result of the different per-transaction rates and monthly fees of PayPal services, PayPal's fees can add up quickly and become hard to untangle. As a result, it would be extremely beneficial to also track your store's transactions separately, if only to gain a better understanding of how much you pay PayPal each month. This is where Shypyard comes in. With Shypyard, you can integrate your sales channels with an accounting system to make the tracking data easy and automated. For example, scroll to the bottom of this link to learn about how you can send the fees applied to orders in your store to an accounting system like MYOB, to be listed as expenses (read more about MYOB here).

Alternatively, if you would like to learn more about Shypyard as a whole, browse through our homepage.

Get Started Today!

PayPal’s streamlined onboarding process helps their users set up quickly. A new user starts by choosing to set up a business account, instead of a personal one, and entering their email & password. Next, they simply need to follow the step-by-step procedures and fill in information about themself and their business. Afterwards, they would gain access to their dashboard, which lists numerous ways of getting started and setting up central features.


In the end, there is no perfect or correct answer when it comes to payment providers, and PayPal does not need to be your only consideration (in fact, check out our article about Stripe to see other payment provider options!). The important thing is to understand what option is the most suitable for your business. And for many, it is PayPal.

Be the first to hear when we launch!

Thank you! Your submission has been received!
Invalid Email. Please try again.