Within the tomb-garden stands the imposing Isa Khan’s Mosque on a raised plinth. As with the other structures in the complex, the mosque suffered on account of inappropriate repairs as well as loss of architectural elements such as the tile-work on the canopies. Following extensive documentation in 2010, conservation works carried out in 2012 included re-plastering the central dome after removing cement plaster and deteriorated lime plaster. With the dome re-plastered thus removing vegetation growth filling in of cracks on the plaster surfaces and removal of decayed materials the water ingress could be halted and the internal surfaces re-plastered and the stone surfaces cleaned.
All the internal and external wall surfaces of the mosque had cement mortar in the joints which needed to be carefully removed. Cement pointing of the internal wall surfaces has been replaced with lime mortar pointing. After the extensive conservation works were completed at the Isa Khan’s complex in 2013, a detailed documentation was undertaken of all canopies to carefully record existing tiles and discern original patterns. The tile restoration works were carried out on the canopies of Isa Khan Mosque by master craftsmen under the full time supervision of Engineers and art conservator.