•In vitro digestion/Caco-2 cell was used to estimate Cd and Pb bioavailability.•Cadmium and Pb bioavailability were higher in the cooked vegetables.•Bioaccessibility values may overestimate health risks of Cd and Pb in vegetables. The estimation of heavy metal bioaccessibility and bioavailability in vegetables is helpful for human health risk assessment. Using an in vitro digestion/Caco-2 cell model, the bioaccessibility and bioavailability of cadmium (Cd) and lead (Pb) in raw/cooked pakchoi (Brassica rapa L., Chinensis Group) and Malabar spinach (Basella rubra L.) were studied. The effect of the addition of iron, calcium and acetic acid to the samples was also determined. The results indicated that Cd bioaccessibility was higher in the gastric phase and Pb bioaccessibility was higher in the small intestinal phase. Cadmium and Pb bioavailability were 11.2% and 9.4% in the raw vegetables, respectively, and found to be higher significantly than the cooked vegetables with 6.1% for Cd and 3.2% for Pb. The results showed that it will be overestimating the risk of Pb and Cd based on the data of raw vegetables ingestion. Using bioavailability values, average Cd and Pb daily intake by adult were 23% and 28% respectively, of the base bioaccessibility values. Our study will be better understanding the possible health risks of some vegetables base on the bioaccessibility or bioavailability.