In the present study, Amukkara Chooram (AC) a well known herbal medicine was investigated for their antibiofilm efficacy against biofilm of Candida albicans. The biofilm inhibitory concentration of 20 µg/mL of AC showed promising effect by inhibiting the biofilm upto 60%. Morphogenic transition state of C. albicans from yeast cells to hyphal transition was prevented by AC was revealed from light microscopic images. In addition, the inhibition of yeast hyphae was examined in the induction medium supplemented with AC. Consequently, atomic force microscope (AFM) also documented the morphological changes observed during the transition state of C. albicans in the presence and absence of AC. Furthermore, scanning electron microscope (SEM) and confocal laser scanning microscopic (CLSM) images showed reduction in the biomass and thickness of the mature biofilm of C. albicans. In vivo investigation of C. albicans with zebrafish infection model presented the clearance of biofilm from the epithelium of the intestinal tissues. Later, the histological changes in liver and kidney due to C. albicans infection open up that treatment with AC was able to significantly rejuvenate the tissues. Altogether, the study presents AC as potent antibiofilm agent with potential ability as alternative medicine to treat C. albicans biofilm mediated infections.