Zoho Invoice is an online invoicing software which helps you get your invoicing done. It has all the essential functionalities related to invoicing like estimates, quotes, multi-currency support, online payments, credit notes, customizable invoice templates, an iPhone app for invoicing on the go, a web app(beta version) for invoicing from android & other mobile devices and multi-lingual support.

Zoho Books on the other hand is a comprehensive online accounting softwarethat lets you get your accounting done online. With Zoho Books you can keep up with the your income and expenses, manage your banking and credit card transactions and work with your accountant online. Within Zoho Books you will see a comprehensive invoicing module which includes all the features of Zoho Invoice, except for the ones listed below:

• Late Fee option is not available in Zoho Books.
• APIs are not supported for Zoho Books now but will be available soon.
• Localization is not yet done (Zoho Books is available only in "English").
• No iPhone or Android apps for Zoho Books at the moment.

Here is our blog to let you know the difference between Zoho Invoice and Zoho Books : here