This study aims to compare the classification of foods available in the Portuguese market using Nutri-Score and NOVA classifications and to analyse their ability to discriminate the fat, saturated fat, sugar, and salt content of foods. A sample of 2682 food products was collected. The nutritional quality of foods was established using the Nutri-Score, classifying them into five categories (from A to E). The NOVA classification was used to classify foods according to the degree of food processing into unprocessed/minimally processed foods, processed culinary ingredients, processed foods, and ultra-processed foods (UPF). The nutritional content of food products was classified using a Multiple Traffic Light label system. It was observed that 73.7% of UPF were classified as Nutri-Score C, D, and E, 10.1% as Nutri-Score A, and 16.2% as Nutri-Score B. Nutri-Score was positively correlated with NOVA classification (ρ = 0.140, p < 0.001) and with the Multiple Traffic Lights system (ρTotal Fat = 0.572, ρSaturated Fat = 0.668, ρSugar = 0.215, ρSalt = 0.321, p < 0.001). NOVA classification negatively correlated with the Multiple Traffic Lights system for total fat (ρ = -0.064, p < 0.001). Our findings indicate the presence of many UPFs in all Nutri-Score categories. Since food processing and nutritional quality are complementary, both should be considered in labelling.