Abstract Background Protein maldigestion and malabsorption lead to malnutrition and are a feature of exocrine pancreatic insufficiency (EPI). Although it is the current standard, measurement of nitrogen in stool to assess protease activity is indirect. Up to 80% of hydrolysed proteins appear in blood in the form of peptides so we developed a method to measure peptide-derived amino acids in plasma as a relevant measure of proteolysis, verified its accuracy, precision, and linearity, and validated it in a porcine model. Materials and Methods We modified a ninhydrin method. Large proteins were eliminated from plasma with 10 kDa-cut-off centrifugal filters. Free and total amino acids were measured in permeate before and after its hydrolysis. Peptide-derived amino acids were quantified by subtracting free amino acids from total amino acids. We verified the method in vitro and by comparing results in healthy and EPI pigs. Results The accuracy of the analysis was close to 100%, with excellent precision (mean relative standard deviation for low, medium and high amino acid levels = 0.88%) and with stringent linearity (r2=0.986, %RE =5.23). The high-throughput ninhydrin method detected levels of peptide-derived amino acids in vivo with maximal changes seen approximately 2 hours postprandially in young pigs. The AUC and Cmax were significantly higher in healthy compared to EPI pigs (p = 0.0026 and p = 0.0037, respectively). Conclusions The high-throughput ninhydrin method is a sensitive, reliable, and practical method for the estimation of dietary peptide-derived amino acids. This assay endpoint could serve as a direct biomarker of protein digestion and absorption.