Soil protein is an important indicator of soil health and for soil health assessments is usually determined using autoclaved citrate extraction (ACE) followed by protein quantification using the Bradford or bicinchoninic acid assay. Here, we investigated an alternative extraction process using microwave-assisted citrate extraction. We show that protein yield increases as the extraction time increases, but that yields comparable to those obtained using the standard ACE method can be obtained with an extraction time as short as 15 min. To the best of our knowledge, this is the first report of microwave-assisted extraction being used to determine this soil protein pool.