The in situ fortification of vitamin B12 (VB12) in foods through fermentation is an effective strategy to address the deficiency of this micronutrient, and precise monitoring of VB12 production is crucial for developing VB12-fortified functional foods. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) is advantageous for analyzing trace substances in food due to its high sensitivity. In the present study, an LC-MS/MS method capable of rapidly and accurately quantifying three active forms of VB12, namely adenosylcobalamin (AdoCbl), methylcobalamin (MeCbl), hydroxocobalamin (OHCbl), in 8 min were developed. Meanwhile, the quantitative result of this method is not affected by pseudo-VB12 because the selected ion channels include fragments of active VB12. Maintaining light-shielding during extraction and purification is essential, as light exposure during the process can decrease the content of detected VB12 by about 30%. At last, the developed method was applied for the determination of VB12 in fermented rice bran and the cell mass of Propionibacterium freudenreichii. The results showed that AdoCbl was the predominant form of VB12 during fermentation, and the addition of cobalt did not influence the proportions of the three VB12 types. The present study reported a rapid and accurate method for the simultaneous determination of three active forms of VB12, which can effectively support the development of foods with VB12 fortification.