The Cerasus humilis kernel is a by-product of Cerasus humilis fruit processing after removing the pulp. Cerasus humilis kernels have abundant nutritional value, while high content of amygdalin limits the deep processing of Cerasus humilis kernels. This study aimed to establish a simple and fast way to degrade amygdalin using lactic acid bacteria to ferment and convert amygdalin into other substances. Lactobacillus paracasei and Lactobacillus acidophilus were directly fermented using the nutrients of Cerasus humilis kernel, and the degradation effect could reach 84.78 % and 71.73 %, respectively. In addition, the substances produced by amygdalin during fermentation were inferred by identifying the degradation products. A novel biotransformation pathway for amygdalin was established, providing ideas for the comprehensive utilisation of the Cerasus humilis kernel. Display omitted •Cerasus humilis kernel was fermented by lactic acid bacteria for the first time.•Amygdalin is degraded by low-cost, environmentally friendly microorganisms.•The degradation effect of amygdalin by Lactobacillus paracasei was 84.78 %.