Due to the increasing use and accumulation of petrochemical plastics in the environment and the rapid depletion of natural resources, microbial polyhydroxyalkanoates have great potential to replace them. This study provides new insights in the field of obtaining of polyhydroxyalkanoates (PHAs) from endophytic bacterial strains and applying them as potential biocontrol agents against postharvest diseases of apples. Two strains—Pseudomonas flavescensD5 andBacillus aerophilusA2—accumulated PHAs in amounts ranging from 2.77 to 5.9 g L−1. The potential to use low-cost substrates such as beet molasses and soapstock for PHA accumulation was shown. The PHAs produced by thePs. flavescensD5 strain had pronounced antagonistic activity againstPenicillium expansum(antifungal property = 62.98–73.08%). The use of PHAs as biocontrol agents significantly reduced the severity of apple blue mold, especially in the preventive treatment option.