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Afforestation effectively sequesters atmospheric carbon (C) into soil, with the magnitude of C sequestration being constrained by soil nutrient availability, particularly phosphorus (P) derived from parent material. While microbial communities inhabited within soil aggregates can adjust their composition and metabolic activities in response to afforestation, their effects on soil P availability remain uncertain. Here, we investigated how microbial adaptations within different soil aggregate‐size fractions (fine‐scale soil structure) were upscaled to influence P availability for soil C sequestration following long‐term (around 32 years) afforestation in subtropical China. We found that afforestation generally led to lower accumulation of total P relative to C and nitrogen (N) in soil aggregates, but induced higher P‐ versus C‐ and N‐acquiring enzyme activities (i.e., lower ecoenzymatic C:P and N:P ratios) compared with the croplands. Structural equation modeling analysis further showed that ecoenzymatic C:P and N:P ratios were primarily associated with the abundance of fungi in the macroaggregates (>250 μm), but showed significant correlations with the abundance of bacteria in the <250 μm finer soil particles. These results revealed that microbial community within different soil aggregate‐size fractions developed divergent strategies to overcome P limitation on soil C sequestration and cope with soil C:N:P imbalance following afforestation. Taken together, our work underpins that fine‐scale soil structural effects are important for the mechanistic understanding of soil P availability and their impacts on C sequestration following afforestation. Key Points: Afforestation led to lower P accumulation relative to C and N in soil aggregatesMicrobial P‐ versus C‐ and N‐acquisition efforts were higher under afforested soilsMicrobial adaptations within fine‐scale soil structure mitigated soil P limitation [ABSTRACT FROM AUTHOR]