The potential of plant growth-promoting rhizobacteria (PGPR) to improve plant growth and nutrient acquisition has received increased attention. This study investigated the synergistic effects of combining PGPR Paraburkholderia sp. SOS3 with the addition of inorganic N fertilizer (iN) or a combined application of inorganic N with organic manure-based fertilizer (iNoN) at low and high levels of N fertilization on Macadamia integrifolia seedling growth. We studied plant growth, mineral N in soil-leachate, and media physicochemical and microbial characteristics. Growth of seedlings fertilized with iNoN at high N level (iNoN 100) was enhanced by PGPR inoculation, with an increase of 32% in total biomass and 43% in N uptake, compared with uninoculated seedlings. No significant PGPR effect was observed on growth under low or high inorganic N treatments but PGPR significantly reduced N leaching after 3 weeks of fertilization. We found a positive relationship between media and plant δ15 N and plant N uptake, and a strong increase in microbial-biomass N under the most productive fertilization treatment (iNoN 100 with PGPR), compared with the other N treatments (without or with PGPR). The results suggest that PGPR improves N acquisition by reducing mineral N loss and increasing plant N availability, but that these effects depend on the N form and N level.