Background In Mexico, 35.5% of school-age children were overweight or obese in 2018. The school food environment is important because children spend a significant part of their time at school and consume one-third to one-half of their daily meals there. In 2014, a Federal Government guideline for the sale and distribution of food and beverages in Mexican schools was published (the AGREEMENT) but the extent of its implementation is not known. Methods Descriptive cross-sectional study in a representative, random sample of elementary schools, using the tools of the INFORMAS network. Data collection included: a) an interview with a school authority; b) a checklist of items available in the school canteen; c) a checklist of the school breakfast menu; and d) an evaluation of the physical environment. The main indicators were: percentage of implementation (self-report) of the AGREEMENT and percentage of compliance (researcher verified) with the AGREEMENT (based on tools b and c). Results 119 schools participated (response rate 87.5%), with 15.1% (95%CI 9.2–22.8) of the schools reporting having fully implemented the AGREEMENT. However, only 1% (95%CI 0–5.3) of the school canteens and 71.4% (95%CI 57.8–82.7) of the school breakfast menus fully complied with the AGREEMENT. A variety of sugar-sweetened beverages and energy-dense, nutrient poor products were found in the school canteens. Further, only 43.7% of the water fountains in schools were functional and 23.4% were clean. In only 24.4% of schools had the school authorities received formal training related to the AGREEMENT and in 28.6% of schools had the parents received information about the AGREEMENT. Conclusion The AGREEMENT has been poorly implemented in elementary schools in Mexico. Actions are needed to encourage and support its full implementation to improve the food environment in Mexican schools.