Vitamin supplements (VS) may act as either complements to or substitutes for healthy foods, with distinct implications for nutrition policy. This study investigates that relationship using nationally representative individual dietary intake data from Chile and a causal framework that combines Directed Acyclic Graphs with instrumental-variable models. Results reveal that individuals who do not consume VS typically have poorer diet quality—a pattern particularly pronounced among low-income, time-constrained, and older adults. Further analysis shows no evidence that VS use substitutes for fruit and vegetables, suggesting that supplements complement rather than displace healthy foods. These findings support targeted nutrition policies that promote appropriate VS use among nutritionally vulnerable groups, in combination with food-based interventions, without undermining healthy food consumption.