The tumor-associated microbiota represents a novel cancer hallmark, yet the interplay between diverse microorganisms, such as bacteria, viruses and fungi, and tumorigenesis remains elusive. Gastric cancer (GC) has long been considered a type of microbiome-associated tumor because of the epidemiological identification of Helicobacter pylori and Epstein–Barr virus as key carcinogenic microorganisms. Nevertheless, the detailed molecular and cellular mechanisms by which these microbial infections eventually drive GC are still debated. Furthermore, recent advancements in technology have enabled the identification of an increasing number of novel microorganisms implicated in the pathogenesis of cancer development, especially from the perspectives of fungal ecology and intracellular bacteria, as well as the microbiota ecosystem. Here, we summarize the recent progress in the study of GC-related pathogens, emphasizing the emerging roles of fungal ecology and bacterial‒fungal interactions (BFIs) in gastric tumorigenesis and highlighting new opportunities for developing microbiome-engineered therapeutic strategies for GC.