This study examines consumer preferences for the potential benefits of CRISPR technology using a best–worst scaling (BWS) approach within an online survey of a representative Spanish sample. The BWS discrete choice experiment focuses on seven key environmental and health-related benefits of CRISPR, using tomatoes as a case study. The selected benefits are derived from science-based information and align with the EU regulatory context, following the European Commission’s 2023 proposal on gene-editing technologies. Estimates from a random parameter logit (RPL) model indicate that pesticide reduction is the most highly valued benefit, followed by water saving and health improvement, thereby highlighting the combined influence of environmental and personal benefits on consumer acceptance of genetically engineered food. The significant standard deviations in the RPL estimates reveal substantial heterogeneity in preferences, which is further examined by identifying two distinct consumer segments. While both segments strongly prioritise pesticide reduction, one is primarily motivated by environmental sustainability outcomes, whereas the other places greater emphasis on health and sensory quality improvements. These findings underscore the need for targeted communication strategies to address distinct consumer concerns, rather than a uniform approach.