Abstract
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>BACKGROUND</jats:title> <jats:p> <jats:italic>Sclerotinia sclerotiorum</jats:italic> is a major crop pathogen commonly managed using fungicides. Efficient biological alternatives are needed but it is essential to determine whether a biocontrol agent persists in soil and affects non‐target microbiota. Here, we assessed the environmental fate and the impact of a novel <jats:italic>Bacillus</jats:italic> sp. strain (SCL1) on soil microbial communities from three contrasted agricultural soils. The fate and effects of SCL1 applied at an agronomical (LD) or elevated (HD) dose were compared with a commercial biocontrol product, tebuconazole, and an untreated control. </jats:p> </jats:sec> <jats:sec> <jats:title>RESULTS</jats:title> <jats:p> SCL1 persistence was monitored by selective plate counts and strain‐specific quantitative polymerase chain reaction (qPCR) analysis. After inoculation, SCL1 declined rapidly but remained detectable up to day 168; at late time points the SCL1 population stabilized at low levels [~10 <jats:sup>3</jats:sup> colony‐forming units (CFU) g <jats:sup>−1</jats:sup> in the high‐dose treatment], supporting its long‐term persistence. Treatment effects on microbial community composition were limited: differentially abundant operational taxonomic units (OTUs) represented up to 9.9% of bacterial and 3.8% of fungal communities. Fungal taxa associated with soil functioning increased under SCL1 treatment in some soils; e.g., Mortierellomycetes in Trugny soil (5.7% in control <jats:italic>versus</jats:italic> 10.7% under low‐dose SCL1 at day 56). </jats:p> </jats:sec> <jats:sec> <jats:title>CONCLUSION</jats:title> <jats:p> SCL1 persisted for at least 6 months in soil microcosms and induced small shifts in bacterial and fungal communities, comparable with reference products. These findings support further field studies to evaluate the efficacy of SCL1 against <jats:italic>S. sclerotiorum</jats:italic> in rapeseed crops, as well as its persistence and potential non‐target effects on soil microbiota. © 2026 The Author(s). <jats:italic>Pest Management Science</jats:italic> published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. </jats:p> </jats:sec>