This study investigated the microbial dynamics, diversity, and succession patterns of yoghurt enriched with baobab (Adansonia digitata) fruit pulp during a 15-hour fermentation period. Baobab pulp was incorporated at 10% (w/v) into pasteurized milk, and fermentation was carried out at 45°C. Microbial analyses included serial dilution, cultural characterization, biochemical tests, and molecular identification using 16S and 18S rRNA sequencing. Results showed a progressive and significant (p < 0.05) increase in microbial populations over time. Total bacterial counts rose from 1.2 × 10² CFU/mL at 0 hours to 6.00 × 10⁵ CFU/mL at 15 hours, while Lactobacillus populations increased from 0 to 5.62 × 10⁵ CFU/mL. Fungal counts also increased significantly from 0 to 1.32 × 10⁴ CFU/mL across the fermentation period. The predominant beneficial bacteria identified were Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Leuconostoc sp., confirming active lactic acid fermentation. Fungal isolates included Aspergillus niger, Mucor sp., Botrytis cinerea, and Penicillium maximae. The detection of Staphylococcus aureus suggests possible contamination, emphasizing the need for strict hygiene during processing. Overall, the findings demonstrate that baobab-enriched yoghurt supports robust fermentative microbial activity and contains diverse microbial communities, while highlighting the importance of aseptic production conditions to ensure product safety and quality.