Despite its large number of madrassahs, Khiva appears to contain relatively few mosques and minarets. However a closer look reveals that several of the madrassahs actually contain mosques which are quite different from the traditional domed building flanked by four minarets found in many parts of the Muslim world. Khiva's mosques vary in size and shape but are often built around an aywan and an inner prayer chamber. The aywan (see 'Aywans') provided a cool, shaded place for summer prayers whilst the inner prayer chamber was used in winter, offering more protection from the elements. This style was mainly used in private mosques, such as those in the khan's residences, in madrassahs and in small neighbourhood mosques. Another design is found in Khiva's Juma (Friday) Mosque which was built to accommodate the entire adult male population of the city for Friday prayers. It differs from most other Juma mosques in that its spacious interior is almost entirely covered with no open courtyard.

As the Arabs conquered neighbouring civilisations, they were influenced by different architectural styles and would often seize churches and other places of worship to use as mosques. As a result many of the Byzantine church styles were incorporated into later mosque designs which varied from region to region.

At the same time mosques display certain common features such as a 'mihrab', the niche indicating the direction of Mecca to which all Muslims should pray. The location of the mihrab influences the layout of the mosque which should face in the right direction. Mosques also need a water source for the ritual washing of hands, face and feet before saying the 'namoz', a prayer prayed by Muslims five times a day. They are usually devoid of furniture, except perhaps for the 'mimbar', a raised platform or stairway used as a pulpit for preaching.

During the lifetime of Mohammed the call to prayer was given from the rooftop of his house. Gradually the usage of a tower evolved leading to the minarets of today. According to Vambery, the Sunnites of Central Asia would sing the 'ezan' or call to prayer which was a frightful sin, as it should only have been spoken or intoned. Today only the Sheikier Beg Mosque in Khiva is allowed to function and the 'ezan' is sung from the comfort of ground level, where the benefits of loudspeakers and a long lead mean the mullah no longer has to climb the minaret five times a day. Minarets in Khiva were used not only to call the faithful to prayer but also functioned as lookout points against the marauding Turkoman tribes or the forces of the Bukharan Emir. Minarets also made excellent orientation points for traders wandering through the narrow, winding streets of the Ichan Kala.