Boron-containing materials are increasingly drawing interest for the use in electronics, optics, laser targets, neutron absorbers, and high-temperature and chemically resistant ceramics. In this article, the first investigation into the deposition of boron-based material via electron beam-induced deposition (EBID) is reported. Thin films were deposited using a novel, large-area EBID system that is shown to deposit material at rates comparable to conventional techniques such as laser-induced chemical vapor deposition. The deposition rate and stoichiometry of boron oxide fabricated by EBID using trimethyl borate (TMB) as precursor is found to be critically dependent on the substrate temperature. By comparing the deposition mechanisms of TMB to the conventional, alkoxide-based precursor tetraethyl orthosilicate it is revealed that ligand chemistry does not precisely predict the pathways leading to deposition of material via EBID. The results demonstrate the first boron-containing material deposited by the EBID process and the potential for EBID as a scalable fabrication technique that could have a transformative effect on the athermal deposition of materials.