Primary production needs to transition towards more sustainable systems that reduce environmental impact, mitigate climate change, and ensure healthy food production with limited use of chemical plant protection products, fertilizers, or antibiotics. Rationally designed microbial communities, or engineered microbial consortia, involve the intentional assembly of microorganisms that can underpin more sustainable primary production systems. Rationally designed microbial communities can for example, (i) enhance ecosystem resilience, (ii) improve bioremediation, (iii) enhance industrial processes, or (iv) prevent diseases. In the perspective, we discuss the route towards market applications with a focus on the methodology needed to rationally design microbial communities for applications in the agri-food production systems. Often and approaches are considered as a continuous process that first consider the genomic and then condition to develop microbial consortia. However, host-microbe interactions influence both the microbial community assembly and host phenotypes and need to be considered from an early stage when developing microbial communities. As such, we propose that the route towards market application(s) should, from a technical perspective include (i) the host of interest, (ii) a library of both slow and fast-growing species, and (iii) genomic information about functions present in the selected microbial consortia.