Purple waxy corn (Zea mays L. var. ceritina Kulesh.), or black purple sticky corn, is an edible plant with antioxidant properties according to its rich anthocyanin, phenolic and flavonoid content. This study aimed to determine how purple waxy corn modified drug metabolizing genes (CYP1A2, CYP2C9, CYP3A4, UGT1A6, and NAT2) and a drug transporter (OATP1B1) in human hepatocellular carcinoma (HepG2) and colorectal adenocarcinoma (Caco-2) cells. The cells were incubated with purple waxy corn (125 to 1,000 µg/mL) for 48 h. Cell viability, reactive oxygen species (ROS), aspartate transaminase (AST), and alanine aminotransferase (ALT) levels were investigated. The mRNA expression of target genes was determined by RT/qPCR. Cell viability remained above 80% even at the maximum tested concentration of purple waxy corn (1,000 µg/mL). Expression of CYP1A2 and CYP2C9 was not modified by purple waxy corn in either HepG2 or Caco-2 cells, but CYP3A4 expression was significantly suppressed in Caco-2 cells. At the highest concentration (1,000 µg/mL), purple waxy corn markedly induced expression of UGT1A6 and NAT2 mRNA in Caco-2 cells. Conversely, purple waxy corn suppressed expression of NAT2 at the highest concentration in HepG2 cells. The expression of OATP1B1 was not affected by purple waxy corn in either cell type. Therefore, consumption of large amounts purple waxy corn could cause food-drug interaction via differential modification of CYP3A4, UGT1A6, and NAT2.