Periodic bioinoculations enhance soil aggregate stability through species-specific effects and interactions with the native microbiota

• MF inoculant enhanced soil aggregate stability over time. • Periodic inoculations enhance bacterial over fungal roles in aggregation. • Inoculant efficacy depends on species and timing. • Inoculant-induced shifts in Acidobacteriota correlated with aggregate stability. Microbial inoculants can improve soil aggregate structure, but their effects are often transient due to limited survival. While periodic inoculations sustain microbial populations, their dynamic effects on soil aggregates remain unclear due to complex biotic and abiotic interactions. Here, we investigated the temporal effects of periodic inoculations with three probiotic consortia, MF ( Bacillus megaterium and Pseudomonas fluorescens ), CB ( Azotobacter chroococcum and Azospirillum brasilense ), and MFCB (all four strains), on soil aggregate dynamics, stability, and biophysiochemical drivers over 135 days. Significant temporal changes in soil aggregate fractions and stability were observed, with inoculant-specific effects. MFCB achieved a higher mean weight diameter (MWD: 0.9 ± 0.05 mm) than other consortia at 45 days, whereas MF exhibited the highest MWD (1.2 ± 0.09 mm) at 135 days. MF and MFCB consistently caused higher exopolysaccharide (EPS) production in soil at 10 and 135 days. Conversely, CB significantly reduced EPS (1.23 ± 0.09 mg kg −1 ) and MWD (0.62 ± 0.11 mm) compared to other consortia at 135 days, potentially due to plant root promotion post-inoculation. The native bacterial community, rather than fungi, played a dominant role in increasing MWD by reshaping large aggregates (>1 mm), with most families in Acidobacteriota strongly correlated with MWD shifts. Random forest and path models revealed that inoculants indirectly enhanced stability through keystone taxa shifts within the bacterial community and associated biochemical pathways. These findings indicate that inoculants can improve soil aggregate stability primarily by modulating the native bacterial microbiota, but these effects are highly time-dependent and species-specific.