This study examined how gastrointestinal conditions affect pesticide bioaccessibility and intestinal transepithelial transport of pesticides (difenoconazole, hexaconazole, and spirodiclofen) in humans. We used an in vitro model combining human gastric and intestinal digestion, followed with Caco-2 cell model for human intestinal absorption. Bioaccessibility of three tested pesticides ranged from 25.2 to 76.3% and 10.6 to 79.63% in the gastric and intestinal phases, respectively. A marked trend similar to the normal distribution was observed between bioaccessibility and pH, with highest values observed at pH 2.12 in gastric juice. No significant differences were observed with increasing digestion time; however, a significant negative correlation was observed with the solid-liquid (S/L) ratio, following a logarithmic equation. R ranged from 0.9198 to 0.9848 and 0.9526 to 0.9951 in the simulated gastric and intestinal juices, respectively, suggesting that the S/L ratio is also a major factor affecting bioaccessibility. Moreover, significant dose- and time-response effects were subsequently observed for intestinal membrane permeability of difenoconazole, but not for hexaconazole or spirodiclofen. This is the first study to demonstrate the uptake of pesticides by human intestinal cells, aiding quantification of the likely effects on human health and highlighting the importance of considering bioaccessibility in studies of dietary exposure to pesticide residues.