The mosque was constructed in the period 1646-1653, which was notably later than all of his other Agra Fort contributions (these were commenced in 1627, his first regnal year, and completed in 1638).

When Shah Jahan visited the mosque upon its completion, he was so impressed with the structure that he returned two years later to show two of his sons.

[1] On the western edge lies the main prayer hall itself, a multi-bayed aisle structure supported by twelve-sided piers.

The interior of the prayer hall does not bear much decoration; Asher notes that the use of undecorated marble is typical of Shah Jahan's private religious architecture.

[2][4][1] The Moti Masjid displays much influence from an earlier marble congregational mosque, constructed by Shah Jahan at the Ajmer Sharif Dargah.