This is a business decision based on how you want to accept payments in your store.
- Third party systems like Paypal are fast and easy to set up, and commonly accepted (for instance many ebay buyers and sellers already have Paypal accounts with funds in them). However, the money does not go into your business bank account so if you want to transfer it out you’ll need to wait while the money transfers and clears into your account. This means you’ll need additional funds to pay for your other business expenses like postage.
- Merchant accounts have a more in-depth process because there are two parts to set up: the merchant account with your bank and the gateway account with the gateway provider (banks do offer both services if you want to keep everything with one place). Money goes directly into your business bank account so can be used for your business expenses.
You will need to look at the combination of setup costs, fees and benefit of getting money directly into your bank account in deciding what is best for you.