Knowledge of the impacts of prescribed burning on ecosystem functions could help to improve forest management practices. However, relative to forest safety and aesthetic values, changes in soil properties and processes after prescribed burning are not well understood. This study aimed to quantify changes in soil microbial communities and greenhouse gas emissions following prescribed burning in a subtropical suburban forest. The soil microbial communities were determined with the Illumina sequencing methods. Carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) emissions were quantified under three different soil water contents, and net greenhouse gas emissions were derived from emissions of the three gases after 7 days of incubation and expressed in CO2-equivalent. Prescribed burning had negligible impacts on soil bacterial and fungal community diversities but significantly changed soil microbial community structures. Compared to the unburnt soil, the relative abundances of Chloroflexi increased by 86% and 119% one month and three months after the prescribed burning, respectively. However, the relative abundances of Mortierellomycota decreased by 94% one month after prescribed burning. At different soil water contents, The CO2 and N2O emissions during a 7-day laboratory incubation did not differ consistently or significantly between the soils collected before/after the prescribed burning. Simultaneously, there were no significant changes in net greenhouse gas emissions from soil in association with the prescribed burning. The results revealed that relative to the unburned soils, prescribed burning caused minor alterations in net soil greenhouse gas fluxes, despite short-term evident changes in soil microbial community structures.