The use of microorganisms in agriculture and food is a very broad issue that faces many challenges. The scientific literature on sustainable agriculture is characterised by four main trends: (1) the role of microorganisms in the transformation, degradation, and recycling of organic matter [1]; (2) the use of microbes as biostimulants and biopesticides, as an alternative to chemical agents [2,3,4]; (3) understanding the soil microbiome and microorganisms interrelationships using modern imaging techniques and algorithms, and the use of microbial consortia for specific applications [1,3]; and (4) plant–microbiome interactions that ensure plant health [5]. Microbiological preparations or vaccines for use in agriculture may contain monocultures or consortia of living microorganisms that are well understood and safe, and which can contribute to the growth, health, and development of the host plant [2]. The use of such beneficial microorganisms is not only an important tool for supporting crop health and productivity, but an effective alternative to the use of agrochemicals [6]. In essence, microbiological products for agriculture are based on the same active substances (living microorganisms) that are produced in similar industrial processes (fermentation, formulation), are managed and used in a similar way, and are intended to have a beneficial effect on a given crop/host. Research on soil biodiversity has seen rapid development, including that on new biostimulants and pools of specific genes, thanks to new omics tools, including genome sequencing (NGS) and metabolomics techniques, which have a direct impact on the dynamics of the agricultural sector [7]. Key topics concerning the role of microorganisms in food include (1) further development of fermentation processes, including the genetic improvement of strains; (2) the improvement of techniques for identifying microorganisms and their metabolites; and (3) the detection of pathogens in production processes [8,9]. Microbial fermentation, a practice more than 7000 years old, is a basic method of producing a variety of food products. During fermentation, microorganisms such as bacteria, yeasts, and moulds are used to convert carbohydrates into various metabolites. In various, often perishable, food products, fermentation contributes to preservation and the improvement of sensory characteristics, nutritional quality, and safety [10,11]. Existing and changing consumer preferences are driving new ideas and development opportunities for the fermented food and beverage sector. Consumers are looking for products that they perceive as natural and wholesome, free from artificial ingredients, handmade, and environmentally friendly [12]. Among such foods, functional products containing health-promoting additives, including probiotic microorganisms, paraprobiotics, postbiotics, and minimally processed products, stand out [13,14,15,16,17]. Fermented foods can be consumed as a non-invasive method of managing various disorders and diseases (including hypertension, diabetes, and hyperlipidaemia, among others) due to the release of bioactive compounds, enzymatic transformations, and probiotic activity [14,18]. Among key innovations in the field of food fermentation are advances in fermentation technologies aimed at increasing efficiency, product range expansions, and the promotion of sustainable development [10].