The scrolls are made from several sheets of parchment that were sewn together. After the sheets were prepared, the scribe used a sharp utensil, or sometimes ink, to mark the columns and lines. The writing was presumably done with pens made of sharpened reeds or hard metal. Most of the scrolls were written with black ink made of soot, resin, oil, and water, although a few contain several lines or words in red ink. Small pieces of leather or pottery shards inscribed with meaningless words, names, or isolated letters bear witness to the scribes' custom of practicing their writing before commencing work.

The majority of the Qumran scrolls are written in Hebrew, though some are in Aramaic and a few in Greek. The letters usually dangle below the guidelines, though in certain texts they are positioned at a slight distance from the lines. Most of the Hebrew and Aramaic scrolls are written in the "Jewish" script, which was widely used in the Second Temple period. In some scrolls, however, the Tetragrammaton or the entire text is in ancient Hebrew script. There are also several phylacteries and mezuzot that are written in micrographic letters, which are no more than two millimeters high. In addition, many texts written in cryptographic script were found; these deal with secret aspects of the sectarians' world.