Bhagwan Bahubali Temple, covering an area of around 4000 sq. feet, is also a special attraction of Mangalayatan complex. The temple houses a white marble statue of Bhagwan Bahubali in standing posture. The 7'3" high statue stands on a 24" high lotus platform. The temple also has statues of Muniraj Bahubali and Muniraj Bharat in standing postures.

Design of Bahubali temple is the same as the Mahavir temple. The hall of the temple has been adorned with portraits of Dharsenacharyadev and Muniraj Padmaprabhamaldharidev. These portraits have been engraved on 4' x 4.5' sized marble panels. Marble slabs of 4' x 2' size, engraved with the text of the 7th Adhikar (chapter) of Acharyakalpa Pt. Todarmalji written Shri Mokshamarga-prakashak and Pt. Daulatramji written Shri Chheh-dhala, have also been fixed on the walls of the temple.

The Bahubali temple will also house a small library and a research institute until their spacious individual buildings, proposed to be built in the second phase of development, are ready.