Abstract Background: Biotin and folate are B-group vitamins that play a critical role in numerous metabolic reactions, and they are supplemented to infant and adult nutritional formulas as free biotin and folic acid. Objective: We describe a rapid method for the analysis of biotin and folic acid that is applicable to liquid milk, milk powders, infant formula, and milk-based nutritional products. Methods: Samples are autoclaved, centrifuged, filtered, and analyzed by HPLC–MS/MS, with quantitation accomplished by the internal standard technique. Results: The method was shown to be accurate, with acceptable spike recovery (biotin: 96.5–108.2%; folic acid: 92.6–104.4%), and no bias (α = 0.05) against either a certified reference material (biotin: P = 0.70; folic acid: P = 0.23) or established analytical method (biotin: P = 0.10; folic acid: P = 0.48) was found. Acceptable precision was confirmed with repeatability relative standard deviation (RSDr) and Horwitz ratio (HorRat) values (biotin: RSDr = 0.5–5.6%, HorRatr = 0.1–0.6; folic acid: RSDr = 2.0–3.1%, HorRatr = 0.3–0.5). Method detection limit and ruggedness experiments further demonstrated the suitability of this method for routine compliance testing. Conclusions: This rapid method is intended for use in high-throughput laboratories as part of the routine product compliance release testing of biotin and folic acid in the manufacturing of infant formulas and adult nutritional products.