The Society's holdings include over 3,000 manuscripts in Sanskrit, Arabic, Persian, Urdu and Prakrit from all over India and Nepal. They are mostly on paper, but some are on palm leaf. They include technical literature on linguistics, medicine, astronomy, Jaina and other brahmanical literature in Sanskrit, an appendix on Buddhist manuscripts, Jaina literature and manuscripts in Gujarati, Hindi and Marathi. Apart from the variety of topics covered, some of the manuscripts are distinguished for their fine calligraphy and paintings. The latest addition to the manuscript collection is the entire work of Pu La Deshpande donated by him.

Some rare manuscripts in the Library
- Aranyakaparvan of Mahabharata, (illustrated Sanskrit) 16th century 
- Divina Comedia by Dante Alighieri (Italian) 1350 AD 
- Gautampricchasutra (Prakrit) with Sanskrit vritti of Sritilaka 1350 AD
- Ganaratnamahodadhi of Vardhaman (Grammar, Sanskrit) Samvat 1423 
- Kalpasutra of Bhadrabahu (illustrated, Sanskrit) Jain manuscript 15th century AD
- Mahabharat by Faizi (Prose translation) (Persian) 18th century copy 
- Prajnaparamita astasahasrika (illustrated, Sanskrit) Buddhist manuscript from Nepal
- Risalat at,tarjamat az-zahira li firqati Bohrat al-bahira An essay on the History of the Bohras (Arabic) 17th century AD 
- Sadavasyaka sutra with Balavabodha (Old Gujerati) 1393 AD 
- Shahnama of Firdausi (Persian) copied in 1843 AD 
- Suryasiddhanta with bhashya of Candelvara (Astronomy, Sanskrit) 12th century AD
- Vasupujyacharita Life of the Jain Tirthankara Vasupujya (Sanskrit) 1242 AD