Verticillium dahliae causes severe yield reductions in a variety of important annual crops worldwide. Control of verticillium wilt has relied on soil fumigation; however, the use of the main soil fumigant, methyl bromide, has been banned in the European Union since 2010, creating a demand for novel crop protectants. As such, the use of biocontrol agents (BCAs) is an appealing management strategy. Prerequisites for the development of a successful BCA are an understanding of the modes of action of the antagonist, its ecological fitness and an efficient and economically feasible delivery system. Therefore, two BCAs (Paenibacillus alvei K165 or the nonpathogenic Fusarium oxysporum F2) and two release strategies (seed coating or amendment of the transplant soil plug) were assessed against verticillium wilt of aubergine (eggplant). Mixing the transplant soil plug with K165 or F2, at a rate of 10 and 20% (v/v), respectively, reduced verticillium wilt symptom development. Furthermore, a positive correlation was revealed between the release strategy and the BCA rhizosphere population. Correlation analysis also showed that disease severity was negatively correlated to the rhizosphere size of the BCA population. In addition, qPCR analysis showed that both BCAs induced the expression of the pathogenesis-related (PR) proteins PR1 and PR4 in the stem of aubergines before and after inoculation with V. dahliae in a manner that suggests a link with the rhizosphere size of the BCA population.