Aim of study: This study aimed to investigate the biocontrol potential of Bacillus amyloliquefaciens against Phytophthora cinnamomi infection in Quercus suber (cork oak). Both in vitro and in planta experiments were conducted to assess the effectiveness of B. amyloliquefaciens as a biocontrol agent. Area of study: The microorganism strains, B. amyloliquefaciens and P. cinnamomi, as well as the embryogenic lines of Q. suber used, have a Spanish origin. Material and methods: In vitro experiments involved evaluating the inhibitory effects of B. amyloliquefaciens on P. cinnamomi growth through dual-inoculated agar plates. In planta, dual inoculation tests were performed by co-inoculating plantlets with both P. cinnamomi and B. amyloliquefaciens. Physiological parameters, such as photosynthetic activity, chlorophyll content, and oxidative stress markers, were measured. All experiments were conducted under controlled conditions. Main results: In vitro experiments revealed the inhibitory effects of B. amyloliquefaciens on P. cinnamomi growth. Infected plantlets displayed symptoms of root infection. Dual inoculation tests resulted in plant survival against P. cinnamomi infection. Analysis of physiological parameters indicated variations among treatments and clones, highlighting the distinct response of Q. suber plantlets to the pathogen and underscoring the importance of genetic variability for disease management. Research highlights: This study provides insights into the potential of a strain of B. amyloliquefaciens as a biocontrol agent against P. cinnamomi infection in cork oak. Further investigations are warranted to elucidate the underlying mechanisms of susceptibility and resistance in different clones of Q. suber.