Microbial inoculants are widely accepted as potential alternatives or complements to chemical fertilizers and pesticides in agriculture. However, there remains a lack of knowledge regarding their application and effects under field conditions. Thus, a quantitative description of the scientific literature related to soil microbial inoculants was conducted, adopting a science mapping approach to observe trends, strengths, and weaknesses of their application during the period of 2000–2020 and providing useful insights for future research. Overall, the study retrieved 682 publications with an increasing number during the 2015–2020 period, confirming China, India, and the U.S. as leading countries in microbial inoculants research. Over the last decade, the research field emphasized the use of microbial consortia rather than single strains, with increasing attention paid to sustainability and environmental purposes by means of multidisciplinary approaches. Among the emerging topics, terms such as “persistence” indicate the actual need for detecting and monitoring the persistence and fate of soil microbial inoculants. On the other hand, the low occurrence of terms related to failed studies as well as formulation processes may have limited the overall comprehension of the real potential of microbial inoculants to date. In conclusion, successful application of soil microbial inoculants in agriculture requires filling the fundamental knowledge gaps related to the processes that govern dynamics and interactions of the inoculants with soil and its native microbiota.