Microbial chemical factories utilize engineering design principles to re-build natural production pathways, enabling the precise, quantitative, and efficient synthesis of chemicals. This is achieved through the optimization of synthetic pathways, the reconstruction of biochemical networks, the development of novel components, and the integration of pathways with cellular and environmental contexts. As a transformative approach to chemical production, microbial chemical factories play a critical role in establishing renewable raw material pathways for industrial economic development and advancing sustainable growth. This innovative model has become a strategic priority for technological advancement and industrial competitiveness in developed nations. This industry has expanded into diverse sectors, including pharmaceuticals, food production, chemicals, and energy. To showcase the most recent scientific advancements in the field of microbial chemical production and to promote the evolution of the bio-manufacturing industry, we organized a special issue entitled "Microbial Chemical Factories". This edition features the latest research conducted by domestic scientists, focusing on areas such as the synthesis of material monomers, pharmaceutical intermediates, functional food ingredients, organic acid biosynthesis, and the development and utilization of non-food feedstock. It provides reference and guidance for the further development of microbial chemical factories.