What is difference between manual and online Encumbrance Certificate.

The difference is in the mode of application. For "Manual" you will physically need to approach the sub registrars office. However since most sub registrar offices now conduct business online you may also apply for an encumbrance certificate online. There may be some difference in the manner the document appears however they are both equally valid documents. Feel free to get in touch if we could be of any further assistance to you.