Risk of skin lesions due to chronic arsenic exposure can be further affected by nutrient intake. We prospectively evaluated the association of nutrient intake and gender with incident skin lesions using data from the Health Effects of Arsenic Longitudinal Study (HEALS) in Araihazar, Bangladesh. Discrete time hazard models were used to estimate these effects in stratified analyses based on skin lesion severity. Overall, we observed significant associations between low intakes of various nutrients (retinol, calcium, fiber, folate, iron, riboflavin, thiamin, and vitamins A, C, and E) and skin lesion incidence, particularly for keratotic skin lesions. Associations for vitamins C and E showed significant linear trends. Gender-specific analyses revealed an inverse association between the lowest quartile of nutrient intake and keratotic skin lesion incidence for retinol equivalents, calcium, folate, iron, and fiber among women. Interactions by gender were observed for retinol equivalents (P-interaction = 0.03), calcium (P-interaction = 0.04), vitamin A (P-interaction = 0.03), and riboflavin (P-interaction = 0.04) with the incidence of keratotic skin lesions. Understanding differential susceptibility to skin lesion incidence based on nutrient intake will help researchers develop targeted interventions to prevent health consequences of arsenic poisoning in Bangladesh and beyond.