Background: Currently, there are different food classification systems in order to inform the population of the best alternatives for consumption, considering all the diseases associated with the consumption of products of low nutritional quality. Reports indicate that these forms of labelling warnings correspond to a laudable strategy for populations that do not have the knowledge to discriminate between the wide range of products offered by the food industry. However, recent publications indicate that there may be inconsistencies between the different classification guidelines, and the guidelines that nations should adopt in their food guides are still a matter of debate. In view of this, the present study aimed to evaluate the quantitative and qualitative differences that exist between the NOVA, Nutri-Score and Chilean Front-of-package (FoP) food warning label according to the Chilean basic food basket list. Method: An analytical study was carried out to classify a list of 736 foods according to three different systems, evaluating the distributions according to their methods of classifying the products. Quantitative differences were contrasted for each system, as well as between them, together with an analysis of the dimensions of each system. Results: According to the Nutri-Score classification, the most frequent category was A with 27% (high nutritional quality), followed by D with 22% (low nutritional quality) of the total. On the other hand, the NOVA classification showed that the most frequent categorization was ultra-processed food (NOVA 4) with 54%, followed by unprocessed (NOVA 1) with 19%. Regarding the FoP warning labels, 57% of the foods were categorized as free warning labels, followed by the category of foods with 3 warning labels (23%). Regarding the results of the principal component analysis, the Nutri-Score and FoP warning labels present a degree of similarity in their classification guidelines, being different than the dimension pointed out by NOVA. Conclusion: The present work managed to demonstrate that there are quantitative and qualitative differences between the classification and recommendation guidelines of the Nutri-Score, NOVA and FoP warning labels, finding concrete discrepancies between them.