The aim of this study was to test the effect of an evaluative conditioning (EC) task on implicit food evaluations and choices between healthy and unhealthy food, and whether the effect of the EC task on food choice would be mediated by implicit food evaluations. To induce the EC effect on implicit food evaluations and food choice, images of healthy and unhealthy foods were repeatedly paired with images of positively and negatively valenced faces, the pairing (healthy-positive/unhealthy-negative or healthy-negative/unhealthy-positive) manipulated between participants. Implicit food evaluations were measured using an Implicit Association Task (IAT), and food choice was measured using a food decision-making task consisting of 22 choices between healthy and unhealthy food items. Results showed a direct effect of EC condition on implicit food evaluations, but not on explicit food choice for the whole sample. However, an indirect effect of the EC task on food choice, mediated by implicit food evaluations, was found. Contingency awareness – whether participants were aware that foods were being paired with valenced stimuli – did not affect the strength of the EC effect, nor did attention to the EC task. Surprisingly, emotional eating was found to moderate the effect of the EC task on both implicit food evaluations and food choice, showing that the EC task had an effect only for those who scored low on emotional eating. In conclusion, this study makes a unique contribution to the EC literature by showing that food choice can be altered by conditioning implicit food evaluations, but that this may only work for people who do not score particularly high on emotional eating.