Colloidal phosphorus (Pcoll) in paddy soils can pose a serious threat to the water environment. Biochar amendment not only directly absorb Pcoll to reduce the runoff loss, but also create hotspots for microbial communities which simultaneously affects soil Pcoll. However, despite the crucial role of microorganisms, it remains elusive regarding how biochar and its feedstock types affect the relationships of soil microbial communities and Pcoll in soil matrix (such as at soil aggregate level). To address the knowledge gap, we explored the (in)direct effects of biochar on the soil Pcoll in physically separated fractions including micro- (53–250 μm) and macroaggregates (250–2000 μm). Results showed that straw and manure biochars decreased the soil Pcoll content by 55.2–56.7% in microaggregates and 41.2–48.4% in macroaggregates after 120 days of incubation, compared to the respective control. The fungal communities showed a significantly correlation (0.34, p < 0.05) with Pcoll content in the macroaggregates, whereas the bacterial communities were extremely significantly correlated (0.66, p < 0.001) with Pcoll content in the microaggregates. Furthermore, the partial least squares path model analysis indicated that biochar amendments directly increased Pcoll content (0.76 and 0.61) in micro- and macroaggregates, but the reduced Pcoll content by biochar was mainly derived from indirect effects, such as changed soil biological characteristics carbon (C)/P (−0.69), microbial biomass C (−0.63), microbial biomass P (−0.68), keystone taxa Proteobacteria (−0.63), and Ascomycota (−0.59), particularly for the macroaggregates. This study highlights that to some extent, biochar addition can reduce soil Pcoll content by affecting microbial communities (some keystone taxa), and soil biological characteristics at soil aggregate level.