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The aim of this study was to evaluate the impact of high-pressure processing (HPP) on the long-term storage of chocolate fillings at room temperature, compared with conventional storage at lower temperatures. Dark chocolate fillings were treated at different pressure levels, holding times and stored at 20 °C for 12 months. Unprocessed batches were stored at 4 °C and at −12 °C. Moisture, water activity (aw), pH, colour, G′1Hz and indigenous microflora were measured at 2, 4, 6, 8, 10 and 12 months of storage. Results showed that 600 MPa/20 min processing was the most effective controlling mesophilic group, presenting 3.8 log cfu/g after 12 months of storage, and inactivating moulds and yeasts after HPP treatment. Colour was affected by storage, including a reduction in the L* parameter in all conditions to final values between 37.8 and 39.3, while the a* parameter increased during storage time at −12 °C and 4 °C to final values of around 12, and parameter b* decreased at storage temperature 20 °C to 5.3. Storage time affected the rheological behaviour of HPP-treated samples, increasing G′1Hz from the 2nd to 12th month of storage time to the final values between 1603 kPa and 2139 kPa. Moisture, aw and pH were not affected by HPP treatment nor storage time.