Eukaryotic microorganisms of protechnological interest in food chains represent essential resources for manufacturing fermented foods and beverages, helping to determine the quality and safety of finished products. In the first part of this contribution, an examination of the role of yeasts and filamentous fungi in the various categories of traditional fermented products is proposed, with a particular interest in geographical indications and typical European products. The overview looks at the contribution with respect to the main components of quality: sensorial, nutritional, functional and hygienic-sanitary. The relevance of microbiomes of fermentative interest containing eukaryotic microbes is then discussed, with particular reference to the ex situ preservation practices of microbiomes associated with specific productions, also in the framework of the activities of microbial collections. In fact, the interest in conserving microbiomes to preserve microbiodiversity and their functionality, as also for study their activities and to guarantee adequate biotechnological valorisation, is increasingly evident. This is an important future challenge involving numerous biological resource centers worldwide. Finally, with a series of case studies, the importance of microbiological cross-over is underlined as a driver of innovation in the sector of fermented products, as a strategy for the development of new products and as an element of regionalisation of non-traditional productions. In other words, it is underlined how the preservation, characterisation and enhancement of microbial diversity can represent a reservoir of solutions capable of improving the attributes of existing products, increasing the added value and promoting the design of new foods and fermented beverages. "Gulden Goksen would like to acknowledge the direct support by COST (European Cooperation in Science and Technology; www.cost.eu), in the framework of COST Action CA20128 (Promoting Innovation of ferMENTed fOods; https://fermentedfoods.eu/)."