The tumor-associated microbiome has emerged as a novel hallmark of cancer. Gastric cancer (GC) serves as a paradigm for microbiome-associated carcinogenesis, with well-established roles for specific pathogens such as Helicobacter pylori and Epstein–Barr virus. However, the detailed molecular and cellular mechanisms by which microbial communities drive gastric tumorigenesis remain incompletely understood. Recent technological advancements have unveiled a broader spectrum of microorganisms implicated in GC, highlighting the emerging roles of the mycobiome (fungal microbiome) and bacterial-fungal interactions in shaping the tumor microenvironment. This review comprehensively summarizes recent progress in GC-associated pathogens, with a particular emphasis on how bacteria and fungi contribute to GC through direct carcinogenic effects, modulation of host immune responses, and influencing the efficacy of immune checkpoint inhibitors. We critically analyze the “double-edged sword” nature of the microbiome in GC and discuss the potential of multi-omics approaches to unravel complex microbe-host interactions. Finally, we explore the frontier of leveraging synthetic biology to develop engineered microbes (including bacteria and oncolytic viruses) as novel anticancer therapeutics, while addressing the challenges in translating these strategies into clinical practice. A deeper understanding of the gastric microbiome, particularly the multi-kingdom microbial network, is poised to open new avenues for microbiome-based precision diagnosis and innovative therapies for GC management.