Malaria remains a major global health challenge, caused by five Plasmodium species—P. falciparum, P. malariae, P. ovale, P. vivax, and P. knowlesi—and transmitted by female Anopheles mosquitoes. Emerging evidence highlights that the interactions between malaria parasites and the host microbiome critically influence parasite survival, growth, and transmission. Both the bacterial communities within the mosquito midgut and the human microbiota can either promote or inhibit parasite development, affecting mosquito feeding patterns, infection risk, and disease severity. Understanding the role of the microbiome in malaria pathogenesis has garnered increasing attention, as these host-microbe-parasite interactions are key determinants of infection establishment, parasite virulence, and clinical outcomes. Insights into how specific microbial communities modulate malaria transmission and disease severity can inform the design of novel prevention and control strategies, including microbiome-targeted interventions. This review synthesizes current evidence on the significance of human and vector microbiota in malaria transmission dynamics and disease severity. Highlighting these complex interactions provides a foundation for innovative approaches to malaria control and contributes to global efforts aimed at reducing the burden of this parasitic disease.