Peat pore network architecture is a key determinant of water retention and gas transport properties, and has therefore been hypothesized to control redox conditions in and greenhouse gas emissions from peat soils. Yet, experimental proof of the impact of the pore network structure on biogeochemical reactions remains scarce. Here, we report on a ¹³C pulse-chase assay developed to functionally explain and visualize the cm-scale heterogeneity in greenhouse gas emissions in peat cores. We injected a ¹³C labeled substrate (¹³C₂-acetate) at different depths in the peat cores and monitored its conversion into CO₂ and CH₄ and the subsequent transport to the core headspace. We then measured the pore network architecture of the same cores by X-ray microtomographic imaging and constructed the air-filled pore networks using pore network modeling. We found large heterogeneity among the replicate cores and injections, indicating the effects of cm-scale heterogeneity on biochemical processes and gas transport. This heterogeneity was largely present at the core (10 cm) and within-core (cm) scale heterogeneity whereas little additional variance occurred on the stand (>10 m) scale. Deeper injections resulted in a smaller faction of the label being converted to CO₂ and this fraction being emitted more slowly from the peat cores. Greater peat air-filled porosity was and pore network metrics could not explain the fraction of label converted to CO₂, but greater porosity as well as higher clustering coefficients and betweenness centrality were associated with slower CO₂ emissions.