Developing analytical methods to assure and control the quality of amino acids has long been a challenge for food ingredient, dietary supplement, and pharmaceutical industries due to the high polarity and the absence of chromophores in many amino acids; the situation worsens further by the lack of information of impurities that could potentially be introduced during the manufacturing processes. Herein we utilize a four-step strategy including impurity identification, method development, sample analysis, and targeted impurity detection and quantitation to demystify the impurity profiles of amino acids. The effectiveness of the approach is highlighted using histidine as an example. Analysis of histidine manufacturing and degradation processes led to the identification of 12 potential impurities of histidine, including amino acids (arginine, lysine, asparagine, aspartic acid, alanine, and glycine) and non-amino acid impurities (histamine, histidinol, 4-imidazoleacrylic acid, 4-imidazoleacetic acid, β-imidazolelactic acid, and urea). A HILIC method using Poroshell 120 HILIC-Z column (2.1 × 100 mm, 2.7 µm) and a mobile phase system consisting of ammonium formate buffer at pH 3.2 in water and 0.1% formic acid in acetonitrile coupled with a single quadrupole mass spectrometer was developed for the detection and quantitation of the proposed impurities. Evaluation of 11 commercial histidine samples using the developed method revealed distinct impurity profiles, as a fingerprint for each sample; seven of the 12 proposed impurities were detected in histidine samples tested. The developed method was evaluated in terms of specificity, linearity, range, accuracy, precision, and sensitivity (LOQ: 2.5–60.6 ng/mL) for its suitability for compendial applications. Given the high degree of overlap between the proposed and the detected impurities, the approach could be utilized to strengthen USP standards for controlling the quality of histidine. Extension of the strategy to the analysis of other amino acids is currently underway. Display omitted •Implementation of a four-step strategy for impurity profiling of histidine.•Potential impurities of histidine were proposed and verified in actual samples.•A HILIC-MS method for the determination of 12 amino acids and non-amino acids impurities was developed.