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The effectiveness of biological commercial products based on <i>Bacillus amyloliquefaciens</i> strains was evaluated through in vitro and in vivo experiments against <i>Plenodomus tracheiphilus</i>. The activity of bacterial cells, volatile organic compounds (VOCs), and culture filtrates of bacteria were tested in vitro against different isolates of <i>P</i>. <i>tracheiphilus</i>. Afterwards, the virulence of these isolates was evaluated on <i>Citrus volkameriana</i> plants to select the most virulent isolate to use in the in vivo experiments. To evaluate the effectiveness of products, <i>C</i>. <i>volkameriana</i> seedlings were pre-treated, twice with biological products and once with standard fungicides, before pathogen inoculation. Moreover, in order to determine the endophytic ability of the bacteria, the population density within the treated citrus stem was determined. Comprehensively, bacterial cells, filtrates, and VOCs were able to significantly reduce the average mycelial diameter of <i>P</i>. <i>tracheiphilus</i>, with some variability according to pathogen isolate. In planta experiments showed that the biological products on average were less effective than fungicides, although all formulates were able to significantly reduce disease incidence and symptom severity, except <i>B. amyloliquefaciens</i> strain D747 (Amylo-X) for symptom severity (SS) 20 days after inoculation. Bacteria were re-isolated from the internal woody tissue of treated plants, showing strong endophytic ability. This work is important as commercial biological products based on <i>B. amyloliquefaciens</i> strains could represent a promising and sustainable alternative for the integrated management of mal secco disease.