Calves are born with a naïve immune system and undergo many stressful events in early life contributing to a higher risk of disease, especially disorders of the gastrointestinal tract. Antibiotics are often used as a first intervention in calves with diarrhea, however, these treatments are not appropriate for most cases given that the majority of diarrhea is caused by viral and protozoal pathogens. The rise of antimicrobial resistance has highlighted the need for antimicrobial alternatives leading to an emerging research field investigating nutritional supplementation of microbial-based products to improve gastrointestinal health in calves. In the past 5 years it has been shown that gut microbial colonization during early life plays a role in immune and metabolic development of calves. Thus, calf production could benefit from the ability to control gut microbiota through supplementation of microbial-based solutions at strategic points. So far studies have shown that microbial based products can impact microbial diversity, gut integrity, and natural defenses that modulate the pro and anti-inflammatory response locally in the gut. Evidence is also mounting that a variety of probiotics and prebiotics namely yeast products, have been effective in improving calf health and performance. These beneficial results have been more recently reported with non-Saccharomyces yeasts, such as Yarrowia lipolytica, and have specifically shown promise. Additional research has found that maternal supplementation of microbial based solutions, in particular probiotics with pre or post biotics, can encourage early maturation of the adaptive and innate immune system of offspring. It is important to note that microbial-based solutions will not replace proper management on-farm, but can complement the practices to maximize the probability for efficacy. Also, the concentration, the time period and the specificity of microbial based solutions introduced in the diet are essential to consider for achieving the best results on-farm. In review, there is a positive future in the field of microbial-based product supplementation for young calves and more strategic use of specific microbial-based products should be at the forefront of research and application.