Keepers of the Faith is set within a small Muslim sect of India, ruled by an avaricious priesthood that demands absolute submission while enforcing archaic social customs. When a section of the community rebels, it is summarily excommunicated, shunned by friends and family and denied religious rites. The peaceful community is split into two.

The novel follows the fates of two blissful young lovers, Akbar and Rukhsana, in the historic city of Udaipur. When the communal split occurs, their families are on opposite sides; the lovers' dream of a happy life together is shattered, and they are forced into separate destinies. Akbar, from the rebel group, goes on to become a writer and family man in Mumbai, while Rukhsana gets married to an immigrant engineer from the United States fanatically devoted to the priesthood.

Years later, Akbar's and Rukhsana's paths cross again. Much has changed and much has not, and they are presented with soul-destroying choices about the rest of their lives.