Arginine is a secondary source of nitrogen in many plant and fungal species. Non-lethal mutations that impact arginine catabolism could cause secondary impacts on the metabolome as cells adjust to the lack of nitrogen availability via arginine. In this study, 1H nuclear magnetic resonance spectroscopy (NMR) was used to compare the metabolomes of Neurospora crassa grown in either minimal medium or arginine-supplemented medium. A strain deficient in the arginase enzyme responsible for catalyzing the first step of arginine catabolism were metabolically distinct from wild-type or urease strains grown under the same conditions. Arginase knock-out strains also exhibited small changes in the composition of the amino acid pool, particularly alanine, when grown in minimal medium.