Achieving a secure and sustainable energy future is one of the greatest scientific, technological and societal challenges of our time. The projected doubling of world energy consumption within the next 50 years, along with our current dependence on nonrenewable fossil fuels, as well as the attendant detrimental effects on the environment that their utilization entails, point to the critical need of alternative energy sources as well as to the more efficient use of existing energy resources. The traditional fossil fuels such as coal, natural gas and oil rely heavily on the energy storage within the form of chemical bonds. A modern society must be able to store and convert large quantities of clean energy derived from solar, wind or other sustainable sources, as well as converting existing fossil fuels in a more efficient and sustainable way. This PhD thesis focuses on the use and development of advanced (scanning) transmission electron microscopy techniques, especially in-situ methods, for energy applications. Specifically, the intent is to understand materials properties and reaction mechanisms of fuel cell catalysts and novel lithium-ion battery and lithium-sulfur electrode materials, so as to enhance the performance of practical devices. Three topics will be discussed (i) advanced electron microscopy for electrochemical energy storage and conversion systems: from ex-situ to in-situ; (ii) catalysts for proton exchange membrane (PEM) fuel cells; and (iii) materials for advanced lithium-sulfur batteries.