Plant-endophyte partnership is a promising approach for remediation of soil contaminated with organic pollutants. Besides environmental conditions, the inoculation method can influence the survival and colonization of an applied microorganism and ultimately phytoremediation efficiency. It is therefore important to assess the efficiency of different inoculation methods and the persistence, colonization, and activity of an applied microorganism in different compartments of the plant and the contaminated soil like rhizosphere, root and shoot. The aim of this study was to assess whether inoculation mode affects survival and colonization, plant growth, and phytoremediation activity of the endophytic bacterium Burkholderia phytofirmans PsJN. Ryegrass was planted in diesel-contaminated soil and inoculated with B. phytofirmans PsJN by four methods: seed inoculation, soil inoculation, rhizosphere inoculation, and foliar inoculation. B. phytofirmans PsJN inoculation generally improved plant biomass production and hydrocarbon degradation. Among the four inoculation methods, soil inoculation was found to be the most efficient in improving plant biomass production, hydrocarbon degradation, and toxicity reduction. Enhanced plant growth, hydrocarbon degradation, and toxicity reduction were correlated with the population of the inoculated strain in the rhizo- and endosphere of the host plant. This study revealed that besides the plant-growth-promoting and pollutant-degrading activities of an inoculated strain, the inoculation procedure plays a vital role in determining the success of phytoremediation.