Aim To gain deeper insights into the clostridial community dynamics and chemical transformations during the ensiling of alfalfa. Methods and Results Direct‐cut alfalfa silage (with the dry matter content of 240 g kg−1) was prepared with or without the addition of a lactic acid bacterial inoculant and sucrose. Silages were sampled at 0, 3, 7, 14, 28 and 56 days after ensiling and their bacterial community was determined using high‐throughput sequencing with a special focus on the clostridial community. A clostridial fermentation occurred in the control silage, with high contents of acetic acid, butyric acid and ammonia nitrogen and Clostridia counts; while the inoculated silage was well preserved, with low pH and high lactic acid content. Lactic acid bacteria dominated the bacterial community during the ensiling process. In the control silage, Weissella confusa, Lactobacillus brevis, Enterococcus mundtii and Pediococcus acidilactici were identified at the beginning of the fermentation. Thereafter, W. confusa, Lactobacillus helsingborgensis and Bifidobacterium asteroides appeared and quickly prevailed. In the inoculated silage, Lactobacillus plantarum dominated the whole ensiling process. The genus Clostridium dominated the clostridial community, and was depressed with the inoculated treatment. Clostridium perfringens, Garciella sp. and Clostridium baratii were the main initiators of the clostridial fermentation of the control silage, while Clostridium tyrobutyricum became the most abundant Clostridia with prolonged ensiling. Overall in the inoculated silage, little changes in the clostridial community were observed throughout the ensiling period. Treating alfalfa silage with a homolactic acid‐based bacterial inoculant prevented a clostridial fermentation resulting in more efficient fermentation. Conclusion Distinct changes in the bacterial community with a special focus on the clostridial community were associated with the development of the clostridial fermentation during the ensiling of alfalfa. Significance and Impact of the Study High‐throughput sequencing based on a novel Clostridia‐specific primer set proved a potentially useful tool to study the clostridial community dynamics, and could aid to elucidate the mechanism by which the clostridial fermentation develops during the ensiling of alfalfa.