Background: This study evaluates the effectiveness of adding a diet smartphone application to standard counseling to modify dietary composition over the long term (12 months). Methods: A randomized, controlled, multicenter clinical trial was conducted involving the participation of 833 subjects from primary care clinics (415 to the intervention (counseling + application) group (IG) and 418 to the control (counseling) group (CG)). Both groups were counseled about a healthy diet and physical activity. For the 3-month intervention period, the IG was also trained to use a diet smartphone application that involved dietary self-monitoring and tailored feedback. Nutritional composition was estimated using a self-reported food frequency questionnaire. Results: An analysis of repeated measures revealed an interaction between the group and the percentages of carbohydrates (p = 0.031), fats (p = 0.015) and saturated fats (p = 0.035) consumed. Both groups decreased their energy intake (Kcal) at 12 months (IG: −114 (95% CI: −191 to −36); CG: −108 (95% CI: −184 to −31)). The IG reported a higher percentage intake of carbohydrates (1.1%; 95% CI: 0.1 to 2.0), and lower percentage intakes of fats (−1.0%; 95% CI: −1.9 to −0.1) and saturated fats (−0.4%; 95%CI: −0.8 to −0.1) when compared to the CG. Conclusions: Better results were achieved in terms of modifying usual diet composition from counseling and the diet smartphone application compared to counseling alone. This was evaluated by a self-reported questionnaire, which indicated an increased percentage intake of carbohydrates, and decreased percentage intakes of fats and saturated fats.