The increasing popularity of avocado (Persea americana) fruit has led to a rise in environmental impacts of avocado production. There is an urgent need to adopt sustainable nutrient practices in avocado nurseries and orchards to reduce nitrogen (N) pollution without compromising productivity. However, there is little understanding of how avocado rootstocks respond to different N fertilisation strategies. We investigated the effects of a plant growth-promoting rhizobacterium (PGPR) from the genus Paraburkholderia on growth of Reed avocado seedlings fertilised with either inorganic N fertiliser (iN) or combined inorganic N with organic manure-based fertiliser (iNoN). We studied plant growth and N acquisition, mineral N (NH4+-N and NO3−-N) in leachate, potting-mix physicochemical properties, and rhizosphere microbial communities. PGPR increased N uptake efficiency (NUpE) in seedlings fertilised with iNoN by 23% compared with iNoN without PGPR, 120% compared with iN without PGPR, and 71% compared with iN with PGPR. No significant differences in growth or mineral N leaching were observed between the iNoN and iN treatments. However, both uninoculated and PGPR-inoculated plants with iNoN fertiliser had greater plant N uptake and rhizosphere microbial-biomass N than uninoculated plants with iN fertiliser. Potting medium with iNoN fertiliser had higher N retention than with iN fertiliser, regardless of PGPR inoculation. Our results provide evidence that PGPR effects on N uptake efficiency are regulated by N form and N availability. The beneficial effects of PGPR inoculation when co-applied with a combination of inorganic and organic N fertiliser indicate that PGPR-based technologies can improve nitrogen recovery in avocado nurseries.