The data set contains measurements of methane (CH4) emissions and their δ13C values at vegetation removal experiments consisting of three vegetation treatments (intact vegetation, vascular plants removed, all vegetation removed). We took pore water samples for DOC, concentrations and δ13C values of CH4 dissolved in the pore water and measured the peat temperature, each at 7, 20 and 50 cm depth in the peat profile outside of as well as within each vegetation removal area. Additionally, we determined the leaf area index of each vascular plant species present at our sampling sites and measured the water table depth. One complete set of measurements consisted of manual chamber CH4 flux measurements at five spatial replicates of the plot cluster consisting of the three vegetation treatments. Each chamber measurement was performed once under light and once under dark conditions. In summer 2021 each measurement was additionally performed under single and double shading of the measurement plot. Pore water sampling and peat temperature measurements were performed once in an area of intact vegetation and once within the area where vascular plants had previously been removed at each of the five spatial replicates. Water table depth was measured once per spatial replicate. Such measurement sets were collected at the hollow microtopography type of Siikaneva bog in South-Western Finland, in July, August and October 2021 as well as in May, July, September and October 2022. Data on CH4 dissolved in the pore water is available only from the 2022 campaigns. We combined CH4 flux measurements on vegetation removal experiments with pore water concentrations and isotopic data to identify the seasonal change in the components of CH4 fluxes (production, oxidation, transport pathways) as well as in their environmental and ecological controls.