Mediterranean diet (MD) is potentially one of the best diets regarding health benefits and sustainability. However, it is faced with serious difficulties staying alive, even in traditionally Mediterranean regions. The objective was to evaluate the effectiveness of an application (e-12HR) to improve adherence to the MD (AMD) in university students. This study was a controlled, randomized, and multicentric clinical trial with two parallel groups (control group (CG) and intervention group (IG)), a 28-day follow-up period, and 286 participants (74.1% women). There were two versions of e-12HR: ‘feedback’ e-12HR (IG) and ‘non-feedback’ e-12HR (CG). Only the ‘feedback’ e-12HR had two specific automatic functions: 1. Evaluation of the user’s AMD; 2. Identification of the food groups for which the user has not fulfilled the MD recommendations. Both versions of the application allowed the collection of data on dietary intake in order to calculate the AMD. When comparing CG and IG at 14-, 21-, and 28-days follow-up (no significant statistical differences at baseline), there were significant statistical improvements in favor of IG in AMD index (0.71, 1.56, and 1.43 points, respectively), and in the percentage of participants with medium/high AMD index (14.4%, 20.6%, and 23.7%, respectively). In conclusion, e-12HR could improve AMD among university students.