Fermentation is derived from a Latin word fermentum, a process of chemical changes in an organic substrate by the action of microbial enzymes. The science of fermentation is called as zymology, and the first zymologist was Louis Pasteur. Study of fermentation is called as fermentation technology. Fermenter or bioreactor is the heart of fermentation technology where the whole study is involved. It is a container with biomechanical and biochemical environment that controls the transfer of oxygen, nutrient to the cells, and metabolic products from the cells. There are different types of fermenters like stirred tank fermenter, airlift fermenter, bubble column reactor, fluidized-bed reactor, packed bed reactor, and membrane bioreactor. There are different processes such as batch, continuous, and fed batch or semi-continuous. Secondary metabolites are produced either through submerged or solid-state fermentation process during the stationary phase of an organism. These metabolites are showing a rising demand in food, cosmetics, drugs, and other industries. The production of these metabolites can be improved by strain improvement through mutagenesis and r-DNA technologies. This chapter focuses on all these areas in detail.