The bioavailability of nitrogen (N) in soil relies on the progressive breakdown of necromass protein to peptide and amino acid components and conversion to inorganic N forms. We understand the fluxes and pathways of the N cycle downstream from amino acids, but our understanding of the factors controlling peptide and amino acid mineralization, particularly in arid soils, is lacking. We investigated the influence of temperature on the rate of dissolved organic carbon (DOC) and nitrogen (DON) cycling in three agricultural soils from Saudi Arabia. Although the physical and chemical properties of the soils differed markedly, phospholipid fatty acid (PLFA) analysis revealed they had similar topsoil and subsoil microbial communities. Soils behaved similarly in terms of the rate of substrate use, microbial C-use efficiency, and response to temperature. Substrate mineralization rate increased with temperature with more C being allocated to microbial catabolic rather than anabolic processes. Our results show that climate change is likely to lead to changes in soil organic matter turnover and shift C allocation patterns within the soil microbial community. This is expected to reduce soil quality and exacerbate nutrient losses. Management strategies are required to promote the retention of organic matter in these soils.