The main writing material was leather, mostly sheep and goatskin, or papyrus, all specially prepared by craftsmen. The leather used for some of the scrolls found in the caves was probably treated in the two tanneries, one at Qumran and the other at nearby Ain Feshkha. Being more durable, leather was preferred for literary works, especially for biblical manuscripts. We have only a single papyrus fragment of a scriptural book (Isaiah). The rabbis later formally prohibited the use of papyrus for copying the Bible. By contrast, letters, deeds of sale, acknowledgments of debt, and non-biblical religious works were often recorded on papyrus.

As a rule, biblical texts were copied on the hairy side of the skin and rolled up with the text inside so as to be protected. Before setting out to write, the scribe lined the leather sheets horizontally with the help of a reed. Papyrus sheets were often covered with writing on both sides and not lined. Contrary to our custom, the Qumran scribes did not write on the lines, but attached the top of the letters to them. Two vertical lines determined the width of the columns. To protect the writing from repeated finger marks on the opening sheet of a scroll, the scribe left a larger first margin blank. 

A sheet usually contained five columns of text. For a longer work several sheets were needed and, to ensure that they would be sewn together in the correct order, their sequence was discretely marked by the scribe. Some of these numberings are still visible. Mistakes were regularly corrected: either erased or signalled by correction dots. Missing words were inserted between the lines or in the margins.

The title of the work was indicated on the verso of the first sheet. Some of these relating to non-biblical texts have survived and consist of the first few words of the document. As a result, the rolled-up scrolls could be easily identified. The scribes used vegetable ink kept in inkwells made of clay or metal, six of which have survived. Ink containing acid damaged the leather as can be seen in the scroll of the Genesis Apocryphon. The copyists wrote with reed pens which they sharpened with the help of a "scribe's knife". 

Most Hebrew and Aramaic Qumran manuscripts were written with the "square" alphabet, which is still in use in modern Hebrew. Twelve biblical manuscripts display the archaic Hebrew alphabet and there are also a few documents employing cryptic scripts. In a number of Qumran scrolls, in order to make it stand out, the four-lettered divine name-YHWH-was written with archaic Hebrew letters, or marked by four prominent dots.