For potato proteins to be used as a food ingredient, the level of natural potato defense substances, the glycoalkaloids (GAs), should be limited. In this work, a method is developed for quantification of the two major potato GAs, α-solanine and α-chaconine, as well as for their aglycon form, solanidine, using liquid chromatography–mass spectrometry single quadrupole in single ion monitoring mode. Standard solutions of GA and a food-grade potato protein powder was used to validate the method. A linear correlation between GA concentration and the ion intensity of >0.995 was obtained for all standard solutions. Recovery of GA in spiked samples was within the range 82%–106%. The method for GA quantification was applied to a variety of potato protein isolates. The results showed that total GA increased during the storage of the potatoes. Washing the potato protein isolates using water at a sufficient level was shown to be able to reduce the amount of GA below the threshold of 150 µg g−1, as needed for human consumption.