Peatlands are susceptible to peat fires, which can lower water levels and cause vegetation changes that modify their ecohydrology and carbon storage capacity. Burns Bog is a restored peatland ecosystem located in Delta, British Columbia, Canada. Following the 2016 fire in the north-western section of the bog, there was an increase in the density of lodgepole pine seedlings. The increase in seedling density is expected to reduce water levels relative to the bog surface (WL), thereby increasing ecosystem respiration (Reco) and decreasing methane flux (FCH4). This study examines the effects of post-fire management—specifically, seedling removal—on Reco and FCH4 within the 2016 burned zone of the Burns Bog. Employing the chamber-portable analyzer technique, Reco, FCH4 and environmental variables were measured from April 2023 to March 2024 at six study sites. These sites encompassed three ecosystem types, each with a paired treatment comparison (with and without seedling removal). For all ecosystems, we observed that sites with seedlings removed typically had lower Reco and higher FCH4 with increased WL, compared to sites with seedlings left in place. Two-way analysis of variance (ANOVA) demonstrated significant effects of seedling removal on Reco, with no significant effects of ecosystem type, whereas both seedling removal and ecosystem type exhibited significant effects on FCH4. This study suggests seedling removal as a targeted ecological restoration strategy can return Reco and FCH4 dynamics to pre-fire conditions in peatlands, which has wider implications for peatland ecohydrology and climate regulation.