Lead (Pb) and decabromodiphenyl ether (BDE209) are the main pollutants at electronic waste (e-waste) recycling sites (EWRSs), and their potential toxic effects on soil organisms have received extensive attention. However, the impact on soil microorganisms of joint exposure to the two chemicals remains almost unknown. Therefore, indoor incubation tests were performed to explore the adverse impacts of Pb and BDE209 on soil microbial activities and chemical transformation for the first time. The results have demonstrated that BDE209 was barely degraded in all treated groups, indicating that the presence of Pb hardly affected BDE209 dissipation. The fractions analysis according to Tessier suggested that Pb gradually transformed towards more stable fractions in the slightly alkaline soil, thus reducing the bioavailability of Pb. Additionally, increased Pb doses caused significantly higher bioavailability (p < 0.05), and the same trend was clearly observed after simultaneous exposure to BDE209. Generally, single Pb or BDE209 exposure markedly inhibited (p < 0.05 or 0.01) soil microbial biomass C (C mic), while soil basal respiration (SBR) indicated the opposite response trend (inhibition or stimulation for BDE209 or Pb alone, respectively). Compared to the controls, Pb dramatically (p < 0.01) facilitated soil metabolic quotient (qCO2) during the incubation period. After joint exposure to Pb and BDE209, C mic generally declined with increasing exposure concentration, following certain dose-response relationships. However, SBR and qCO2 were highly significantly stimulated (p < 0.01), and more doses of Pb and BDE209 resulted in higher values. The results of these observations have provided a basic understanding of the potential ecological risk of Pb and BDE209 in soil at EWRSs.