The aim of this study was to evaluate the influence of high hydrostatic pressure (HHP) (400 MPa for 2.5 min and 500 MPa for 1 min) and storage temperature (4 °C and 20 °C), on the physicochemical, rheological and microbiological properties of filled chocolates during storage time. The results showed that the physicochemical (moisture, water activity and pH) and microbiological parameters (total aerobic mesophiles, moulds and yeasts) were particularly affected, at 20 °C, during storage time (P < 0.05). The dynamic rheological parameters (G′ and G″) were not affected by pressure or time of HHP treatment, but were affected by the higher storage temperature especially after 180 d. The mechanical spectra of chocolate fillings stored at 4 °C was the least affected, when compared with the chocolates stored at 20 °C (0.1 MPa/20 °C, 400 MPa/20 °C and 500 MPa/20 °C). Industrial relevance The preservation of traditional filled chocolates can present some hurdles due to the use of perishable raw materials, physical changes during processing, and also to the influence of external factors, which tend to shorten shelf-life. The most important factors that contribute to the shelf-life of filled chocolates include physical properties (i.e. drying, sugar bloom or fat bloom), microbiological stability (i.e. the use of ingredients with high water content will ease the development of moulds and yeasts) and chemical properties (i.e. oxidation of fatty acids or hydrolysis of fatty acids or saponification). The use of HHP in filled chocolates could be an important contribution to improve the food safety of high quality filled chocolates as an alternative to conventional heating treatments or refrigeration.