Waste amendments, such as steel slag and biochar, have been reported as a strategy for improving soil fertility, crop productivity, and carbon (C) sequestration in agricultural lands. However, information regarding the subsequent effects of steel slag and biochar on C cycling and the underlying microbial mechanisms in paddy soils remains limited. Hence, this study aimed to examine the effect of these waste amendments (applied in 2015–2017) on total soil CO2 emissions, total and active soil organic C (SOC) contents, and microbial communities in the early and late seasons in a subtropical paddy field. The results showed that despite the exogenous C input from these waste amendments (steel slag, biochar and slag + biochar), they significantly (P < 0.05) decreased total CO2 emissions (e.g., by 41.9–59.6% at the early season), compared to the control soil. These amendments also significantly (P < 0.001) increased soil salinity and pH. The increased soil pH had a negative effect (r = −0.37, P < 0.05) on microbial biomass C (MBC). The biochar and slag + biochar treatments (cf. control) significantly (P < 0.001) increased SOC contents in the both seasons. The amendments altered the soil microbial community structure that associated with soil C cycling: (1) all three amendments increased the relative abundance of Agromyces and Streptomyces, which was associated with higher soil pH (cf. control); and (2) biochar and slag + biochar treatments caused a higher relative abundance of Sphingomonas, which was supported by high SOC contents under those amendments. Overall, this study demonstrated that the steel slag and biochar amendments altered microbial community composition due to changes in key soil properties, such as salinity, pH and SOC contents, with implications for increasing soil C stocks while mitigating CO2 emissions in the paddy field.