With the increasing application of nanoscale zero-valent iron (nZVI) for in situ soil remediation, its effects on soil functionality and ecosystem need to be thoroughly evaluated. Herein, we investigated the effects of nZVI on CO₂ and CH₄ emissions from uncontaminated and pentachlorophenol (PCP)-contaminated soils and the underlying microbial mechanisms by designing a 68-day anaerobic soil culture experiment; thereafter, the effects of above aged nZVI on soil CO₂ and CH₄ emissions in the following 20 days were further studied. In the uncontaminated soil, 1–10 g/kg nZVI treatments reduced soil CO₂ emission by 17.4–82.6% and increased soil CH₄ emission by 10.8%–119.7%, but these effects disappeared after the nZVI was aged. The emissions of soil CO₂ and CH₄ were significantly inhibited by the PCP contamination (100 mg/kg) mainly due to the toxicity to related soil microorganisms. The applications of 1–10 g/kg nZVI significantly reduced CO₂ emissions from the PCP-contaminated soil by 24.0–86.7%, while 10 g/kg nZVI markedly increased soil CH₄ emission by 1875.4% and restored the methanogenic activity to the control level after the nZVI was aged. The 10 g/kg nZVI treatment enriched hydrogenotrophic methanogen (Methanobacterium) and organics-degrading bacteria by releasing H₂, increasing soil pH, and decreasing soil Eh; the abundance of genes encoding key enzymes (Mcr, Mtr, Hdr, Mta, and Mtb) in all methanogenic pathways significantly increased after the nZVI treatment, indicating that nZVI could have a broad promoting effects on soil methanogenic processes. The findings demonstrate that the addition of nZVI for in situ remediation of organochlorines-contaminated soils will affect soil greenhouse gas emissions and provide basic data for safe nZVI applications.