This study aimed to investigate the effects of citric acid, malic acid, and Lactobacillus acidophilus (L) on fermentation parameters and the microbial community of leguminous Chamaecrista rotundifolia silage. Fresh C. rotundifolia was treated without any additive (CK), or with L (106 CFU/g fresh weight), different levels (0.1, 0.3, 0.5, and 1% fresh weight) of organic acid (malic or citric acid), and the combinations of L and the different levels of organic acids for 30, 45, and 60 days of ensiling. The effects of malic acid and citric acid were similar during the ensiling process. Treatment with either citric or malic acid and also when combined with L inhibited crude protein degradation, lowered pH and ammonia nitrogen, and increased lactic acid concentration and dry matter content (p < 0.05). The neutral detergent fiber and acid detergent fiber increased initially and then decreased with fermentation time in all treatments (p < 0.05). Increasing the level of organic acid positively affected the chemical composition of C. rotundifolia silage. In addition, the addition of 1% organic acid increased the relative abundance of Lactobacillus, while the relative abundances of Clostridium and Enterobacter decreased at 60 days (p < 0.05). Moreover, both organic acids and combined additives increased (p < 0.05) the relative abundance of Cyanobacteria at 60 days of fermentation. We concluded that adding malic acid, citric acid, and L combined with an organic acid could improve the quality of C. rotundifolia silage and increase the relative abundance of beneficial bacteria. The addition of organic acid at a level of 1% was the most effective.