Probiotics have important functions in both human and animal health and nutrition. Probiotic bacteria, yeasts, and fungi are essential elements of the microbiota. These microorganisms that suppress pathogens, improve digestion, support the immune system, and several functions are an irreplaceable part of life. Traditional biotechnology, which entered our lives with domestication, became modern biotechnology after the discovery of DNA and has been advanced with revolutionary techniques in parallel with the developing technology. DNA transfers between living organisms, gene insertion, gene deletion, and gene conversion have become possible by gene engineering. Methods such as induced mutations, recombinant DNA technology, homologous recombination, and CRISPR/Cas are used for this purpose. As in various organisms, probiotics are also manipulated with gene engineering applications. Biotechnological approaches aim to increase the efficacy of probiotics, to give probiotic properties to non-probiotic microorganisms, to obtain products, to develop vehicles for the delivery of pharmaceuticals or vaccines, to manipulate probiotics to combat certain diseases or pathogens and to design probiotics suitable for personalized medicine approach. In this section, after providing general information on biotechnology and probiotics, biotechnological methods that are currently used in the manipulation of probiotics will be discussed.