Today, methane (CH4) and nitrous oxide (N2O) emissions represent 20% of the total greenhouse gas (GHG) inventory worldwide. CH4 is the second most important GHG emitted nowadays based on both its global warming potential (25 times higher than that of CO2) and its emission rates, while N2O is the main O3-depleting substance emitted in this 21st century. However, despite their environmental relevance and the forthcoming stricter legislation on atmospheric GHG emissions, the development of cost-efficient and environmentally friendly GHG treatment technologies is still limited. In this context, an active bio-technological abatement of CH4 and N2O emissions combined with the production of high added value products can become a profitable alternative to mitigate GHGs emissions. The feasible revalorization of diluted CH4 emissions from landfills has been recently tested in bioreactors with the production of ectoine, a microbial molecule with a high retail value in the cosmetic industry (approximately $1300 kg−1), as well as with the generation of polyhydroxyalkanoates (PHAs), a commodity with potential to replace conventional petroleum-derived polymers. This CH4 bio-refinery approach can be also based on the biogas produced from anaerobic digestion, therefore improving the economic viability of this waste management technology. The N2O contained in emissions from nitric acid production processes can be also considered as a potential substrate for the production of PHAs, with the subsequent increase in the cost-effectiveness of the abatement strategies of this GHG. On the other hand, the off-gas N2O abatement from diluted wastewater treatment plant emissions has been recently confirmed, although at the expense of a high input of electron donor due to the need to first deplete the O2 transferred from the emission. This chapter constitutes a critical review of the state-of-the-art of the potential and research niches of bio-technologies applied in a CH4 and N2O bio-refinery approach.