The ongoing climate change in permafrost areas can trigger abrupt thaw processes, leading to the formation of thermokarst lakes and ponds. These water bodies, especially in organic-rich areas, are recognized as strong methane emitters during the ice-free periods and have the potential to accumulate high amounts of methane in and under the ice, which can be released during the ice melt. We estimated wintertime CH₄ storage and daily bottom flux in nine shallow ponds within two permafrost peatlands in Northern Norway, Iškoras and Áidejávri, during the 2023–2024 ice cover season. The wintertime CH₄ storage ranged from 0.6 to 24 g CH₄-C m⁻² and contributed up to 40 % of the annual CH₄ budget at the Iškoras site. The heterogeneity of the CH₄ wintertime accumulation is related to pond depth, differences in vegetation, and the thermokarst pond formation age. The latter has been investigated using a space-for-time substitution approach along chronosequences of thermokarst formation spanning more than 70 years. The winter CH₄ bottom flux increased from 3 mg CH₄-C m⁻² d⁻¹ in two-year-old pond to 107 mg CH₄-C m⁻² d⁻¹ in a pond formed between 30 and 60 years ago. Ponds that formed more than 70 years ago and are currently experiencing sedge regrowth exhibited a high CH₄ bottom flux of 60 mg CH₄-C m⁻² d⁻¹, while older ponds dominated by Sphagnum mosses showed 4 to 10 times lower CH₄ bottom fluxes.