Chocolate is an adequate matrix to deliver bioactive ingredients. However, it contains high sugar levels, one of the leading causes of chronic degenerative diseases. This work aimed to evaluate the effects of milk chocolate reformulation with alternative sugar sweeteners (Sw; isomalt + stevia), probiotics (Prob), and ω-3 polyunsaturated fatty acids (PUFAs) on its physicochemical properties and consumers’ acceptability. Lactobacillus plantarum 299v (L. p299v) and Lactobacillus acidophilus La3 (DSMZ 17742) were added as Prob strains, and fish oil (FO) was added as the source of ω-3 PUFAs. Prob addition resulted in chocolates with >2 × 107 colony forming unit (CFU) per serving size (12 g). Except for Prob, aw values of all treatments were <0.46. Sw and Sw + Prob presented the nearest values to the control in hardness, whereas Sw without FO increased fracturability. FO, Sw + FO, and Sw + Prob + FO contained 107.4 ± 12.84, 142.9 ± 17.9, and 133.78 ± 8.76 mg of ω-3 PUFAs per chocolate, respectively. Prob + FO increased the resistance of chocolate to shear stress, while Sw + FO showed a similar flow behavior to the control. The consumers’ acceptability of Sw + Prob chocolate was adequate, while Sw + Prob + FO had higher acceptability than Prob + FO. Health benefits of reformulated milk chocolates requires further assessment by in vitro, in vivo and clinical studies.