The aim of this study was to investigate the survival of probiotics (Lactobacillus acidophilus NCFM, Lactobacillus rhamnosus HN001 and Bifidobacterium lactis HN019) in milk chocolate masses prepared at temperatures 35 °C and 40 °C. The influence of probiotics and preparation temperature on rheology, particle size distribution and sensory properties of the chocolates, was examined during 6 months of storage at 20 ± 2 °C. An inoculation temperature of 40 °C significantly improves the rheological and sensory properties of probiotic chocolate, as well as leading to the survival of L. acidophilus NCFM and L. rhamnosus HN001 strains. After 6 months of storage, the survival of these strains was above 90%, with a viable cell count of about 8.1 log(CFU g⁻¹). An inoculation temperature of 40 °C provides higher scores of overall sensory quality (4.52–4.68), higher quality category (excellent), lower maximal viscosity (for 1.2 Pa s) of chocolates, than a temperature of 35 °C. Compared to the chocolate without probiotics, those inoculated at 40 °C achieved less increase in volume weighted mean diameter distribution (average 0.8%) than chocolates inoculated at 35 °C. Based on the results reported in this paper, seeding of the probiotics in industrial conditions can be done in the mixing tank (at 40 °C) before the phase of chocolate shaping. Addition of probiotics at this stage facilitates the manufacturing process, improves the overall quality of chocolate and preserves the probiotics as a key component of this type of product.