The distribution of free and bound forms of B-group vitamins (B1, B2, B3, B5, and B6) was quantified in quinoa seeds using LC-MS-TOF combined with a stable isotope dilution assay. The effectiveness of liberating thiamine, riboflavin, nicotinic acid, pantothenic acid, pyridoxal, and pyridoxine from the food matrix and cofactors was evaluated for a variety of extraction conditions, including the addition of enzymes. Phosphatase and protease inhibitors, as well as ultrafiltration, were evaluated for their ability to suppress vitamer liberation via enzymes endogenous to quinoa. Cold extraction, together with a mixture of phosphatase and protease inhibitors, is identified as the most efficient treatment to prevent the conversion of cofactors into simple vitamers. Overnight incubation at 37 °C both with and without additional hydrolytic enzyme preparations containing phosphatase and β-glucosidase activity was almost equally effective in releasing the bound forms of the vitamers. This indicates that the endogenous enzymes within quinoa seeds have high activity. β-Glucosidase should be used when the total pyridoxine content is to be determined, and thermal treatment followed by enzymatic treatment with phosphatase activity is recommended to liberate the bound forms of pyridoxal prior to quantification.