Background: This study aims to compare the antimicrobial activity of theobromine and two commercially available kid's fluoride toothpastes. Materials and Methods: In this in vitro study a chocolate-based nonfluoride toothpaste, Theobromine (Group A) and two commercially available kid's fluoride toothpaste, Kidodent (Group B), Colgate kids toothpaste (Group C) were used in this study. Freeze-dried stock culture of the strains of Streptococcus mutans, Lactobacillus acidophilus, Enterococcus faecalis, and Candida albicans was cultured in their respective selective media. Dentifrices were added to the wells punched out in the culture media and incubated. The zones of inhibition were measured to find out the antimicrobial activity. all data statistically analyzed SPSS using Kolmogorov–Smironov and Shapiro–Wilk's tests. one-way ANOVA was done and Turkey's honest significant difference post hoc test was done for pairwise comparison P ≤ 0.001. Results: Theobromine showed a greater zone of inhibition, which was statistically significant when compared to other two kid's fluoride toothpastes. Conclusion: Theobromine shows more antimicrobial effect against S. mutans, L. acidophilus, and E. faecalis, whereas almost a neutral effect with C. albicans. Theobromine though nonfluoridated toothpaste showed greater zones of inhibition than other commercially available fluoridated kid's toothpastes.