Proton conductivity has been studied thoroughly in two isomeric In(iii)-isophthalate based MOFs. In-IA-2D-1 is capable of showing proton conductivity (3.4 ×; 10−3 S cm−1) under humidified conditions (98% RH), whereas In-IA-2D-2 can conduct protons (2.6 ×; 10−5 S cm−1) under humidified as well as anhydrous conditions. © 2013 The Royal Society of Chemistry.