He continued coaching college football part-time in the Washington area. From 1907 to 1908, Nielsen was the head coach at the George Washington University. In his first year there, the Hatchetites posted a poor 2–5–1 record, but improved to 9–1–1 the following season, which was enough to clinch the South Atlantic Intercollegiate Athletic Association (SAIAA) championship. Nielsen then coached at Georgetown University from 1910 to 1911. In that period, his teams posted a 14–2–2 record and outscored their opponents 438–57. Georgetown's losses came at the hands of undefeated, untied, and unscored upon Pittsburgh and the Carlisle Indians led by Jim Thorpe. Georgetown secured the SAIAA championship both years of Nielsen's tenure. At the same time, Nielsen studied at the Georgetown University Law School, and received a Master of Law degree in 1906.