The number of plant-based dairy alternative products on the market is growing rapidly. In the case of soybean-based yoghurt alternatives, it is important to trace the content of saponins, the phytomicronutrients with a disputable health effect, which are likely to be responsible for the bitter off-taste of the products. We present a new sample extraction method followed by hydrophilic interaction liquid chromatography with mass spectrometric detection (HILIC-MS) for identifying and quantifying soyasaponins in soybean-based yoghurt alternatives. Soyasaponin Bb, soyasaponin Ba, soyasaponin Aa, and soyasaponin Ab were quantified using commercially available standard compounds and with asperosaponin VI as the internal standard. As the recoveries of soyasaponins were unacceptable in yoghurt alternatives at their natural acidic pH, the adjustment of pH was performed as one of the first steps in the sample extraction procedure to achieve the optimum solubility of soyasaponins. The validation of the method included the assessment of linearity, precision, limit of detection and limit of quantification (LOQ), recovery, and matrix effect. The average concentrations of soyasaponin Bb, soyasaponin Ba, soyasaponin Ab, and soyasaponin Aa in several measured soybean-based yoghurt alternatives utilising the developed method were 12.6 ± 1.2, 3.2 ± 0.7, 6.0 ± 2.4 mg/100 g, and below the LOQ, respectively. This method provides an efficient and relatively simple procedure for extracting soyasaponins from yoghurt alternatives followed by rapid quantification using HILIC-MS and could find a rightful application in the development of healthier and better-tasting dairy alternatives.