Traditional clinical and molecular prognostic factors offer valuable insight into the heterogeneous natural history and treatment response of head and neck squamous cell carcinoma (HNSCC) yet fail to explain the full spectrum of observed variability. The tumor microenvironment (TME), comprising microbiome and immune cells can impact treatment response and prognosis. We analyzed The Cancer Genome Atlas (TCGA) to evaluate the association of specific microbes and genes in TME with survival and their differential expression in HPV positive (+) and HPV negative (-) HNSCC. HNSCC RNA sequencing (RNAseq) samples from TCGA were processed through the Exogenous sequencing in Tumors and Immune Cells (ExoTIC) pipeline to identify gene expression and microbial presence. HPV status was assessed by detection of papillomaviridae family of microbes. Clinical data from TCGA was extracted to compare overall survival (OS) and control for competing variables using Cox proportional hazards regression. Difference in immune cell abundance was evaluated by Kruskal-Wallis test. All statistical analysis was performed using R. A total of 498 RNAseq samples from TCGA were analyzed. Oral cavity, oropharynx, hypopharynx, and larynx tumors comprised 21.6%, 15%, 1.8%, and 22.2% of specimens, respectively. HPV was detected in 111 patients (22%), most commonly Alpha papillomavirus 9 (90.1%). Of the 5838 enriched microbes, 330 were significantly associated with OS after controlling for tumor stage, smoking, and age. Specifically, the presence of Alpha papillomavirus 9 was associated with significantly improved OS [adjusted HR = 0.60 (95% CI 0.40 - 0.89, p = 0.01)]. Microbial species found in more abundance in HPV- tumors included Citrobacter farmeri, Thermoanaerobacter kivui and Yersinia pestis which are gram negative anaerobes. Genes related to cellular transport and DNA repair were enriched while genes related to proliferation (e.g., SAGE1) were depleted in HPV+ samples. HPV- tumors had a significantly higher number of M0 (p < 0.001) and M2 macrophages (p = 0.035) while HPV+ tumors had more T regulatory cells (p < 0.001) and CD8+ T-cells (p < 0.001). Tumor microenvironment was significantly associated with survival for HNSCC patients, with particular microbes such as Alpha papillomavirus 9 correlating with improved OS. Greater abundance of certain anaerobic microbes was seen in HPV- tumors. These findings suggest TME can be used to predict patient outcomes and potentially guide personalized treatment approaches. We found an abundance of M0 and M2 macrophages in HPV- tumors, which are considered pro-tumorigenic, while anti-tumor M1 macrophages were similar in the two groups. This may help identify mechanism of resistance to immunotherapies and tailor novel immunotherapy combinations in specific patient subgroups. With further prospective research and external validation these findings have the potential to significantly impact the way we treat HNSCC in the future.