The effectiveness of microwave-assisted protein digestion in different well positions of a 96-well microplate was investigated where microwave-assisted protein digestion of bovine serum albumin was performed in 10 different wells of a 96-well microplate in a microwave oven. Similarly increased sequence coverages (~70%) were generally observed for the 10 microwave-assisted protein digestion samples compared to conventional overnight digestion (63%), which is possibly due to higher miscleavage ratios (~53%) of the samples from microwave-assisted protein digestion than conventional overnight digestion (42.1%). The reproducible results of microwave-assisted digestions from different well positions demonstrate the potential of high-throughput analysis of proteins using microwave-assisted protein digestion.