Plant coexistence and diversity–productivity relationships are often studied separately, yet both are shaped by the same biotic interactions. Here we focus on how host-specificity among soil pathogens and mutualists alters niche and fitness differences among plant species, subsequently modifying biodiversity effects on productivity. Specialist pathogens can generate niche differences through density-dependent processes, thereby stabilizing plant coexistence and enhancing complementarity effects. Specialist mutualists can instead destabilize coexistence and lead to variable effects on productivity. The effects of generalist microbes are less predictable, depending on relationships between plant traits determining microbial interactions (e.g., defense traits) and those determining competitive ability and biomass production. This review underscores the significance of plant–microbial interactions in bridging the mechanisms underlying species coexistence and biodiversity–ecosystem functioning relationships.