The consumption of out-of-home meals is increasing. This study is aimed at assessing the effect of an intervention on healthy offerings and the management of food allergies and intolerances. Ten (control group) and eight restaurants (intervention group) were randomized in a 12-month parallel controlled trial. The outcomes were changes regarding adherence to the Mediterranean diet (AMed) and gluten management (SMAP) criteria, the traffic light rating category, nutrients, and gluten- and allergen-free content of dishes. After 12 months, and compared with baseline, there was an improvement of ≥25% in four items of the AMed criteria in the intervention group, whereas an increase in the offer of dairy desserts without added sugar, and a decrease in the first course offerings of vegetables and/or legumes were observed in the control group (p < 0.05). Also, after 12 months, there was an improvement of ≥50% in four SMAP criteria (p < 0.05) and in the mean average of all SMAP criteria (p = 0.021) compared with baseline in the intervention group, in which intra- and inter-group improvements for desserts in traffic light ratings, nutrients, and allergens were observed (p < 0.05). Therefore, the intervention showed beneficial effects, improving the quality of menus toward the Mediterranean diet pattern and gluten and food allergy/intolerance management.