The overuse of agrochemicals for agricultural productivity to meet the global food demand of the rapidly growing human population is a great environmental threat, particularly for aquatic ecosystems. Being associated intimately with plant health, growth, and productivity, the plant microbiome is emerging as a promising environmentally friendly and sustainable resource for agricultural productivity. For the past decades, our understanding of the interactions between plants and microorganisms and our knowledge of how to improve the plant microbiome by using microbial inoculants has increased significantly. A better understanding of the impact of the plant microbiome on mineral resources will benefit plant and soil health. In this review, we highlight the importance of microbial inoculants and their interactions with mineral fertilizers in enhancing crop productivity, as well as current challenges.