Cold stress, including chilling and freezing temperatures, severely damages crop production and quality during the whole plant life from seed germination to the end of postharvest life. Cold stress can indirectly reduce plant yield and quality by suppressing symbiont growth and, thereby, symbiotic performance. In organic farming, application of bioactive compounds and/or symbiont microorganisms can be used as biostimulants to promote plant performance under normal and stressful conditions. Regulation of bioactive compounds and metabolites (by modifying gene expression, signalling and synthetic pathways) in plants and/or symbionts have the potential to promote plant and symbiont relationships and performance. So far, few studies have shown the effectiveness of regulating symbiont metabolites (for example, Sphingomonas faeni overexpressing 1-aminocyclopropane-1-carboxylate deaminase (ACCD) enzyme 2 activity that enhance cold tolerance), which can be referred to as microbiome breeding, on modulating plant and symbiont performance and stress responses. This review article incentivizes further studies to use microbiome breeding to not only promote symbiont and host tolerance, but also to promote symbiotic performance and, thereby, plant yield and quality, particularly when symbiosis is depressed by undesirable environmental conditions such as cold stress. The efficacy of using biostimulants and cold tolerant symbionts on improving plant metabolites, symbiotic performance, and cold acclimation are discussed in this review article.