Proteins represent a significant reservoir of organic nitrogen in most terrestrial ecosystems and therefore comprise a key component of the soil N cycle. Consequently, there is a critical need to develop robust methodologies for quantifying the abundance of proteins in soil. In this study we evaluated the performance of five commercially available total protein assay kits in a contrasting range of soils. All the kits were based on the detection of proteins after conjugation with either chromophores or fluorophores. Overall, we found that all the kits suffered significant signal interference from humic substances present in solution, resulting in either a quenching or enhancement of the protein response. Inter-comparison of the kits yielded no agreement when quantifying the total amount of protein present in soil solution, with differences in concentration for individual samples ranging 20-500-fold when using the different assay kits. We concluded that none of the commercial assay kits can provide a reliable indicator of soil solution protein content. Although it may detect some non-proteinaceous material (e.g. peptidoglycan), total protein quantitation is currently best undertaken by acid hydrolysis of proteins in solution with subsequent determination of the amino acids liberated. However, there is an imperative need to develop robust methods for protein extraction, purification and analysis in soil.