Three natural antibacterial compounds including bacteriocin like substance (BLS) produced from lactic acid bacteria (LAB), ethanolic extract of propolis (EEP), and nine plant extracts were evaluated against soft rot Bacillus strains. Testing in vivo these compounds were evaluated to control pear and apple soft rot disease. Among eight BLS tested, BLS of LAB2, LAB105 and LAB 107 exhibited the highest antibacterial activity as indicated by the formation of clear inhibition zone. Propolis extracts exhibited significant antibacterial activity against all tested soft rot Bacillus strains and it was noticed that the antibacterial activity was concentration dependent. Among nine plant extracts tested, extracts of Eucalyptus globulus and Psidium guajava exhibited the highest antibacterial activity. All tested antibacterial products significantly decreased apple and pear soft rot severity caused by Bacillus altitudinis compared to untreated control. The highest reduction percentage of soft rot severity was recorded for EEP followed by BLS from LAB and plant extracts tested, respectively. Combined pre-and post-harvest treatments of apple and pear with antimicrobial compounds proved to be more effective in reducing the soft rot severity and improved the physical and chemical properties of fruits during storage in both years of the study. The natural antimicrobial agents used in this study were promising compounds, since it seems to be more safe, economical and great potential for extending the shelf life and improve the quality of fruits. Therefore, the application of these compounds in the control of apple and pear soft rot could be advantageous for consumers, producers, and the environment.