Sourdough plays an important role in quality assurance, especially during developing wholegrain wheat bread products. The value of barley and hull-less barley grains is determined by the low lipid and high carbohydrate (starch and resistant starch) content, balanced amino acid profile, dietary fibre and phenolic compounds. During germination (24 h) the amount of sugar, amino acids and vitamins increase in the grains. Therefore, it could be optimal environment for microbiota growth in sourdough. The goal of the research was to find optimal technological parameters and to study microorganism growth dynamic during the fermentation of sourdough with germinated hull-less barley. The study was performed using three steps of fermentation, with different temperature and time parameters. At each step pH, dynamics of lactic acid bacteria (LAB), yeast-like fungi and total plate count (TPC) growth were determined using standard methods. The results of the study showed that the optimal fermentation conditions for the first stage are 48 h and 26 ± 1 °C, for the second stage 8 h and 26 ± 1 °C and for the third stage 20 h and 28 ± 1 °C. During fermentation of the sourdough, the pH 3.91 is reached, LAB 8.8 log10 CFU g−1, and the yeast-like fungi 8.7 log10 CFU g−1 was determined. Obtained data show that more than 80 bacteria and 50 microscopic fungal species were detected in hull-less barley flour, but after germination their diversity decreased and in the germinated hull-less barley sourdoughs dominated species were Pediococcus pentosaceus.