The bacterial diversity and abundance after three consecutive back-slopping practices applied on homemade yoghurts collected from different villages in Konya province of Türkiye was identified via metagenomic analysis. Additionally, physicochemical, microbiological, and sensory properties were evaluated for all back-slopped yoghurts. No substantial differences were found regarding the acidity, total solid, fat, ash, and syneresis values of the yoghurts while yoghurt A (from Mülayim village) received the highest consumer scores. Predominant phyla shared across all samples were Firmicutes (97%), Bacteriodota (0.40–1.09%), and Proteobacteria (0.23–1.01%). Lactobacillus abundance was determined between 89.12 and 92.12%, 79.92 and 94.95%, and 87.55 and 96.50% in yoghurts A, B (from Körveli village), and C (from Esentepe village), respectively. B2 (69 bacterial OTUs) and C3 yoghurts (54 bacterial OTUs) showed a higher bacterial diversity by Shannon index compared with the others. The results revealed how consecutive three back-slopping affect the microbiota and characteristics of yoghurts.