Broad variations in dietary and physical activity patterns are part of nutritional transition concept. An additional nutritional transition has as main characteristic the change of consumption of processed foods for ultra-processed foods (UPF). This study aims to evaluate trends of UPF availability in Portuguese population and its association with diet-related non-communicable diseases (NCD) health indicators. This ecological study used data from the Household Budget Surveys conducted by the National Statistics Institute each 5 years within a national representative sample of households. The percentage of UPF was calculated based on the total daily amount of food and beverages available per capita (in grams). Data from the years 1990, 1995, 2000 and 2005 were used, which were retrieved from DAFNE-Anemos Software. NCD age-standardised mortality, prevalence and incidence were obtained from the Global Burden of Disease database, for the years 2000, 2005, 2010 and 2015. Between 1990 and 2005, the UPF availability increased from 3·9 % to 13·8 %. Over the years, almost all food and beverages categories increased the UPF availability contribution, mainly noticeable for milk, sugar, cereal and meat products. Positive correlations were observed between UPF availability and digestive diseases both in prevalence (r = 0·062; P = 0·037) and incidence (r = 0·005; P = 0·010) measures. Neoplasms incidence also showed positive correlation with UPF availability (r = 0·002; P = 0·012). Trends in UPF availability in Portugal increased exponentially. At the same time, there is a trend towards a decrease in unprocessed and processed food availability. The Portuguese population should be made aware of the health risks resulting from excessive consumption of UPF.