Soil organic amendments in agricultural production can benefit crop production and a wide range of soil properties, including soil aggregation. Soil aggregate formation is largely driven by microbial activities, and can in-turn influence microbial communities by generating distinct microbial habitats, as well as associated impacts on water and nutrient dynamics. We investigated the long-term effects of two fertilizer management strategies (poultry manure compost vs. mineral fertilizer) and biochar amendment (0 vs. 10 t ha−1 walnut shell biochar, 900 °C pyrolysis temperature, by-product of gasification) on soil aggregation, soil organic C, and microbial community dynamics in water-stable aggregate fractions in corn-tomato rotations. Using wet-sieving, soils (0–15 cm) were divided into four size fractions: large macroaggregates (2000–8000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and silt and clay (<53 μm) for calculation of mean weight diameter in both 2014 and 2018. The total C and microbial community composition and abundance within each fraction were evaluated in 2018. Across all treatments, six years of continuous compost application maintained soil aggregate stability and C storage by increasing soil microbial biomass and associated dissolved organic C. Bacterial and fungal populations under compost treatments were significantly higher than under mineral fertilizer treatments based on 16S rRNA gene copy number and internal transcribed spacer (ITS) abundance, which likely contributed to the formation and maintenance of macroaggregates in compost treatments. Interestingly, continuous application of manure compost may increase microbial available C sources by increasing the abundance of bacteria with the potential to degrade aromatic C as predicted from 16S sequences. Soil under the mineral fertilizer treatment showed decreases in the proportion of large macroaggregates, bulk soil C, and aggregate-associated C storage compared to the compost treatment. The application of highly recalcitrant walnut shell biochar had limited long-term impacts on soil aggregation and C dynamics, likely due to its lack of microbially-available C and limited interaction with the soil environment. Our results indicate that continuous compost inputs maintained soil structure and associated physical stabilization of SOM by enlarging soil microbial available C pool, higher soil microbial biomass, and increasing aggregate formation. The soil aggregate structure, in-turn, generated diverse habitats and altered soil microbial communities. Compost inputs, in addition to or in partial replacement of mineral fertilizer inputs, can provide valuable microbial-driven ecosystem services, such as carbon storage and soil structure, while still providing fertility for crop growth.