Most snacks displayed at supermarket checkouts do not contribute to a healthy diet. We investigated the effects of introducing healthier snack alternatives at checkouts in supermarkets on purchasing behavior. In Study 1, we investigated the effect of completely substituting less healthy with healthier snacks (one supermarket). In Study 2, we investigated the effect of placing and discounting healthier snacks while the less healthy snacks remain in place (two supermarkets). In both studies, the number of purchased snacks (per 1000 customers) was used as the outcome variable. Results for Study 1 showed that the absolute number of purchased checkout snacks was 2.4 times lower (95% confidence interval (CI): 1.9–2.7) when healthier snacks instead of less healthy snacks were placed at the supermarket checkouts. Results for Study 2 showed that when additional healthier snacks were placed near the checkouts, the absolute number of healthier purchased snacks increased by a factor of 2.1 (95% CI: 1.3–3.3). When additional healthier snacks were placed near the checkouts and discounted, the absolute number of healthier purchased snacks increased by a factor of 2.7 (95% CI: 2.0–3.6), although this was not statistically significant higher than placement only (ratio: 1.1, 95% CI: 0.7–1.9). Purchases of less healthy snacks did not decline, and even slightly increased, during the intervention period (ratio: 1.3, 95% CI: 1.1–1.5). If supermarkets want to promote healthier snack purchases, additional healthier products can be positioned near the checkouts. However, this does not discourages the purchase of less healthy snacks. Therefore, to discourage unhealthy snack purchases at supermarket checkouts, a total substitution of less healthy snacks with healthier alternatives is most effective.