After the communal meal, the sectarians returned to their tasks. Some studied sacred texts, delving into the books of the Pentateuch and the Prophets and attempting to reveal through exegetical methods the "divine secrets" of Jewish law, history, and the cosmos. While certain books were brought into the community by new members, others were composed or copied by the sectarians themselves.

The writing and copying was apparently carried out in several rooms located in the central building. The scriptorium seems to have been located on the upper floor, as attested by the inkwells and broken desks found among the debris of the floor below. Most of the scrolls from Qumran were written on parchment, with a few on papyrus. When a scroll was completed, it was rolled up and bound with a leather strip that was threaded through a tag affixed to the edge of the scroll. The scrolls were stored in this manner, ready for study. The room to the west of the scriptorium may have served as a classroom or reading room, as suggested by the benches that run along its walls. The room adjacent to it has been identified as a library.