Although the houses in the village varied in size they followed a fairly standard plan. The first room very often contained a rectangular mud brick structure, partially or completely enclosed except for an opening on the long side, which was accessed by three steps. Bruyère found remains of these structures in twenty-eight of the sixty-eight houses he knew of on the site.

The function of the bed-like structures is still debated by Egyptologists. It has been suggested that they could have served as a birthing or nursing bed, or as a bed altar for ancestor worship. Fragments of several paintings from the outer walls of some of these structures deal specifically with themes of female life: labour, childbirth and daily care. It is thought that the villagers may have worshipped deities or prayed to a recently deceased relative in these bed-altars.

It has recently been suggested (Brooker, 2009, pp. 44-53) that the front rooms at Deir el-Medina were used as gardens. This suggestion is supported by the existence of several clay models of houses from other sites in Egypt which show enclosed courtyards within the frontal space. Archaeological evidence suggests that gardens were created at lower levels than the houses. The majority of the floors in the front rooms of the Deir el-Medina houses were at lower levels - some 40 to 50 cm below street level. Textual evidence for the front room and its purpose is limited, but both instructions and love poetry suggest the importance of a private garden to an ancient Egyptian.

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The second room was the main living room and was higher than the first. The flat roof of the room was supported by one or two wooden pillars resting on stone bases. Archaeological evidence suggests that the second room had a sacred significance. Votive stelae have been found near shallow rectangular and vaulted wall niches that occur in several houses in the first and second rooms. Limestone offering tables were found near them. False door dedications were found in the second rooms of most of the houses. All this evidence seems to indicate that the second room was used, among other things, to communicate with and gain protection from those outside the bounds of ordinary mortal existence.

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Some houses had a small chamber off the second room, which seems to have been used both as a general storeroom and as a place to sleep. Beyond this room was a kitchen and a staircase to the roof, which was partly open to allow smoke to escape. Two cellars complete the dwellings.