Delays between soil sampling and processing for analysis are common in both research and agronomy, but the effects of storage conditions on measurements of plant-available nitrogen (N) are rarely considered. With increasing recognition of organic N pools in soils, such as amino acids and peptides, it is necessary to determine how sample handling impacts the outcomes of soil N quantification. In this study, we used in situ microdialysis to approximate plant availability of amino acids, ammonium and nitrate, then compared to both potassium chloride (KCl) extract and microdialysis samples taken from excavated soil samples when in the field, after 24 h refrigerated storage, and after storage for 1 month, either refrigerated or air-dried. Nitrate levels measured with microdialysis and KCl extracts increased immediately after soil sampling and continued to accumulate in the next day and 1 month stored samples. Amino acid and ammonium measurements remained more constant; however, microdialysis showed a decline in amino acid-N between in situ and next day samples. The proportional representation of N pools in the in-field extracts was most similar to in situ microdialysis. Soil samples should be processed for N analysis as close to sampling as possible, and the storage duration and conditions reported. The influence of storage must be considered in interpreting soil test results.