Unhealthy diets are prevalent in Western countries, especially among low-educated people. To have an effect on health, it is important that dietary changes are sustained over time. This study examines long-term effects of a cognitive and environmental-feedback version of a Web-based computer-tailored (CT) nutrition education intervention targeting fruit, vegetables, high-energy snacks and saturated fat. A randomized controlled trial was conducted with a basic (tailored intervention targeting individual cognitions and self-regulation processes; n = 456), plus (additionally targeting environmental-level factors; n = 459) and control group (generic nutrition information; n = 434). Participants were recruited from the general population and randomly assigned to a study group. Online self-reported questionnaires assessed fruit, vegetable, high-energy snack and saturated fat intake, self-regulation, self-control, and Body Mass Index (BMI) at baseline and nine-months post-intervention. Linear mixed model analyses examined group differences in change over time. Educational differences were examined by group X time X education interaction terms. Effects were examined in the total sample and among participants who did not comply with dietary- or BMI guidelines. The effects on vegetable intake in the total sample differed according to educational level (p = 02). Among low/moderate-educated participants, the basic version was significantly more effective in increasing vegetable intake than the control program (effect size (ES) = 0.32) and plus version (ES = 0.22). No effects were found for high-educated participants. Self-regulation change was significantly larger in the control group than in the basic (ES = 0.18) and plus (ES = 0.16) group. In general, both intervention versions did not result in long-term intervention effects. The exception was an effect of the basic version on self-reported vegetable intake among low/moderate-educated adults in the total sample. More research is needed on how targeting self-regulation processes and environmental-level factors in Web-based CT nutrition education interventions can increase long-term efficacy. Netherlands Trial Registry NTR3396 .