Zoho Invoice is integrated with payment gateways like PayPal, GoogleCheckout, Authorize.Net, PayPal Payflow Pro, Stripe and 2Checkout. These integrations let you receive online payments for your invoices via these payment gateways. All you need to do is configure the Payment Gateway in your 'Settings' and insert the 'Online Payment URL' in the invoice notification email that you'd send to your customer.
For more information, see the online payment gateways help section.
Zoho Invoice FAQ