Background HPV-positive and HPV-negative head and neck squamous cell carcinomas (HNSCC) differ in clinical behaviour and treatment response, yet the early microenvironmental changes driving these differences remain unclear. Objective To define how HPV16 E7 expression shapes tumour–stromal–immune dynamics during early carcinogenesis. Methods we employed a stepwise -nitroquinoline-1-oxide (4NQO) carcinogenesis induced model in wild-type (WT) and HPV16 E7-expressing (K14E7) transgenic mice to recapitulate the initiation and progression of human HNSCC. Tongue epithelium was profiled longitudinally across defined stages of disease progression, corresponding to normal epithelium, early lesions, and advanced dysplasia/carcinoma, using single-cell RNA sequencing (scRNA-seq). Disease severity was concurrently assessed using a structured clinical severity grading system grading system based on lesion progression, enabling integration of molecular changes with phenotypic disease stages. This approach allowed characterisation of tumour microenvironmental dynamics across clinically relevant stages of carcinogenesis. Results HPV16 E7 expression established a distinct baseline tissue state prior to carcinogen exposure, characterised by increased epithelial proliferation and an immune-enriched microenvironment. During carcinogenesis, these baseline differences were associated with divergent trajectories between WT and K14E7 tissues. HPV-associated samples demonstrated sustained immune engagement, dynamic epithelial state transitions, and coordinated stromal remodelling, consistent with a reprogrammed tumour–immune interface from early stages of disease. Conclusion HPV fundamentally reshapes the tumour microenvironment before tumour formation, driving distinct evolutionary trajectories during HNSCC development. These findings provide a potential biological basis for differences in disease progression and therapeutic response between HPV-positive and HPV-negative tumours.