Immediately upon rising, the community members washed themselves, dressed, and hurried down the paths leading from their dwellings to the central building, in order to observe together the commandment of daily morning prayer. Evidence of the community's morning prayers is found, for example, in a hymn in the Psalms Scroll (Column XIX). Its sequence and vocabulary have much in common with the preliminary morning service (birkhot hashahar) in normative Jewish liturgy.

The sectarians at Qumran appear to have worn phylacteries during prayers, and certain members may have even worn them all day. The phylacteries found at Qumran represent the oldest phylacteries known to date. Their external form, the parchments they contain, and the method by which they were fastened resemble the phylacteries used today, made in accordance with the rabbinic prescription. However, while the external form of phylacteries appears to have been standardized during the first century CE, it seems that the regulations concerning the contents of the phylacteries had not yet been established at the time the Qumran phylacteries were made. This is attested by the fact that some of the Qumran phylacteries contain the four usual textual excerpts arranged in a different order, while others even contain additional passages, such as the Ten Commandments.