Biological control agents and plant growth promoting rhizobacteria (PGPR) are widely applied as a substitute to chemical pesticides and fertilizers. In the current study, we characterized the plant growth promoting and biological control agent Paraburkholderia tropica bioactive secondary metabolites. Furthermore, we evaluated the in vitro plant growth promoting related functions and biological control activities against Ralstonia solanacearum and Fusarium oxysporum. Gas chromatography-mass spectrometry (GC-MS) analysis of the ethyl acetate extracts of bacterial culture supernatant proposed the potential production of cyclohexanone, tetradecanol, and octadecane which are considered antimicrobial compounds with activity against plant pathogenic bacteria and fungi and have a positive outcome on plant growth of tomato seedlings. Root colonization ability was determined on tomato plant roots using viable bacteria counts of rifampicin resistant mutations generated for Paraburkholderia tropica isolate, while the colonization was confirmed and localized via scanning electron microscope (SEM). Paraburkholderia tropica isolate tested in this study and its extracted bioactive secondary metabolites can be used as an environmentally friendly substitution of chemical fertilizers and fungicides against fungal phytopathogens.