The effect of endophytic Bacillus subtilis (strains 10-4, 26D) and their compositions with salicylic acid (SA) on some resistance and quality traits of stored potatoes infected with Fusarium dry rot were studied. The experiments were carried out on hydroponically grown Solanum tuberosum L. tubers that were infected before storage with Fusarium oxysporum and coated with B. subtilis 10-4, 26D with and without exogenous SA, and then stored for six months. It has been shown that 10-4, 26D, 10-4 + SA, and 26D + SA reduced in different levels (up to 30–50%) the incidence of F. oxysporum-caused dry rot (with the highest effect for 10-4 + SA). SA notably enhanced the positive effect of 10-4, while for 26D, such an effect was not observed. All of the tested treatments increased amylase (AMY) and AMY inhibitors activity in infected tubers, while decreased Fusarium-induced protease activity (except in the case of 10-4 + SA, which promoted a slight increase) was revealed. 10-4, 26D, and their compositions with SA decreased (in different degrees) the pathogen-caused lipid peroxidation, proline, and reducing sugars accumulation in potatoes after long-term storage. It was also discovered 10-4 and 26D, regardless of SA presence, decrease pathogen-induced glycoalkaloids α-Solanine and α-Chaconine accumulation and preserved increased levels of starch and total dry matter in infected stored potatoes. The findings indicate endophytic B. subtilis and its compositions with SA is a promising eco-friendly and bio-safe approach to cope with postharvest decays of potato during long-term storage; however, when developing preparations-compositions it should take into account the strain-dependent manner of B. subtilis action together with SA.