Cheeses exist since ancient times and are still a matter of discovery, as well as a source of innovation. Originally designed to preserve milk, their culture- and tradition-driven technology led to the empirical selection of domesticated microbial consortia. Science has later deciphered, cultivated and characterized the members of such dedicated consortia. Microbial strains can now be selected based on both technological and probiotic criteria. Beyond the traditions and the expected hedonic perceptions, the keystones of the current changes in cheese technology are indeed the way cheeses are made, the way starters are selected and conserved as well as how the cheeses are destructured in the digestive tract, according to specific population. Here we describe our advances in these different research areas and the emerging trends for future. The selection of strains of lactic acid bacteria and of propionibacteria, each combining cheese-making and probiotic skills, leads to the production of functional cheeses, in which the dairy matrix constitutes a protective delivery vehicle for immunomodulatory components. This is illustrated in the context of colitis, i.e. gut inflammation. Cheeses enriched in whey proteins, fermented with selected starters, fulfil the requirements of elderly towards essential aminoacids. Uncoupling the 2 major steps of cheese making, texturing through protein concentration, and flavouring through microbial fermentation, allows quick, safe and sustainable production of “high-tech” cheeses with reduced energy consumption and reduced coproducts production. Incorporation of vegetable proteins, and of microbes able to process them, into the cheese-making process, leads to innovative cheeses with a reduced ecological impact. All these innovations open new avenues for the development of designer cheeses adapted to evolving needs of specific populations and addressing growing ethical concerns.