One strategy for the prevention and treatment of non-communicable diseases (NCDs) is the implementation of the front-of-pack labeling (FoPL) in foods and beverages. In 2020, Mexico adopted the warning label system (WL) as a new public health policy, whose aim is to help consumers make healthier food choices. Previously, the Guideline Daily Amount (GDA) was the labelling used it. This paper aims to compare the understanding of two FoPL, the GDA and the WL, through the identification of unhealthy products in Mexicans with NCDs. We analyzed data from 14,880 Mexican adults older than 20 years old with NCDs (overweight-obesity (OW/O), self-reported diabetes mellitus 2 (DM2), or/and hypertension (HT), or/and dyslipidemia (Dys)). Participants were randomly assigned to one of two groups: the GDA labeling or WL. Each group had to respond to a survey and had to classify food products images as healthy or unhealthy according to the labelling system to which they were assigned. The correct classification was determined according to the criteria of Chile's labeling nutrient profile stage 3. To evaluate the correct classification in each one of the groups we evaluated the differences in proportions. Logistic regression models were used to assess the likelihood to correctly classify the product according to participants' number of diseases and WL information, taking GDA label as a reference. Participants who used the information contained in the GDA label misclassified food product labels in greater proportion (70%), mostly participants with three or more NCDs (participants with OW/O+ HT+ Dys, represent 42.3% of this group); compared with those who used WL (50%). The odds of correct classification of food products using WL image were two times greater compared to GDA image in participants with NCDs; being greater in participants with three or more NCDs. The study results highlight the usefulness of WL as it helps Mexicans with NCDs to classify unhealthy food products more adequately compared with GDA.