Background <p>Amino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (<i>Pinus radiata</i>) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants.</p> Results <p>Amino-acid fertigation notably increased shoot biomass, plant height, and root collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts coincided with higher needle auxin, a plausible link that merits testing. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency.</p> Conclusions <p>Our findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also associated with a shift in the root mycobiome, including taxa often considered beneficial, thereby offering a sustainable pathway to nursery production of radiata pine.</p>