Peatlands represent massive global carbon (C) pools and sinks. Carbon accumulation depends on the ratio between net primary production and decomposition of organic matter, both of which can change under projected increases of atmospheric carbon dioxide (CO2) and N deposition or after peat cutting. Significant areas of peatlands have been damaged by drainage and peat harvesting worldwide. After abandoning exploitations and spontaneous regeneration, these secondary peatlands can become major C-sinks but also important methane (CH4) sources. As the atmospheric concentration of methane, a greenhouse gas (GHG) of major importance, has more than doubled during the past 200 years, identifying factors regulating the flux of CH4 and CO2 into the atmosphere is crucial. This research focuses on the microbiological and ecological aspects of biodegradation (decay) occurring in abandoned cutover peatlands. This work is based on complementary fields such as plant eco-physiology, soil biology and biochemistry, microbial and molecular ecology and biogeochemistry. Initially, we described the gas exchange occurring between these ecosystems and the atmosphere and concluded that peatlands could sequester carbon during their regeneration, although not without emitting important quantities of methane. This brought us to consider the aerobic decomposition of plant litter. Decomposition was not only influenced by changes in produced plant litter quality but also more directly through micro-environmental conditions. Aerobic biodegradation creates the substrate for methanogenic microorganisms responsible for methane production. On the whole, these used acetate as a substrate for methanogenesis and were numerous in early peatland regeneration stages. In pioneering stages of regeneration, acetate production could be maintained by important contribution of homoacetogenic bacteria. Methane diffuses through the waterlogged peat and is turned into CO2 by methane oxidising bacteria in the upper layers. These bacteria, with various oxidation efficiencies, were shown to have contrasting ecologies in relation to vegetation type. Their abundance and distribution is also strongly linked to the emission of greenhouse gases. The common denominator of all these processes is the nature of the organic matter itself which plays a dominating role in the carbon transfer, energy transduction, and control of its own biodegradation.