The aim of this study was to investigate the fate of the most common Alternaria toxins found in wheat—tenuazonic acid (TeA), alternariol (AOH), and alternariol monomethyl ether (AME) during sourdough processing. For this purpose, spiked whole wheat flour, 3% sourdough starter, 0.5% of baker’s yeast, and 105% of water calculated on flour weight as a base were used as raw materials. Spiked whole wheat dough was fermented for 4 h, 8 h, 12 h, 24 h, and 48 h at 25 °C, and at each point the fermented dough samples were taken, frozen, lyophilized, grounded, and stored until further analysis. To study the effect of sourdough processing on TeA, AOH and AME content, the validated method of high-performance liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) for these mycotoxins was used. Mathematical models of Alternaria toxins reduction were developed in the form of Four Parameter Logistic Regression function. The maximum reduction of TeA, AOH, and AME levels was archived at 48 h of dough fermentation at 25 °C compared with dough after kneading (0 h). Under these conditions, a reduction of the toxin levels of 60.3 %, 41.5%, and 24.1% was observed for TeA, AOH, and AME, respectively.