Aflatoxin B1 (AFB1), a potent dietary carcinogen, and Epstein-Barr virus (EBV), an oncogenic virus, are both implicated in cancer development, particularly in endemic regions. However, the combined effects of AFB1 exposure and EBV infection on the epigenetic landscape remain poorly understood. This study investigates the impact of AFB1 and EBV on histone post-translational modifications (hPTMs) in Burkitt lymphoma (BL) cells through an integrative approach combining untargeted mass spectrometry-based profiling and a time-lapse experimental design. Our results reveal subtle, yet reproducible and dynamic alterations in histone methylation and acetylation patterns over time, with EBV-infected cells exhibiting distinct epigenetic responses compared to uninfected cells. Specifically, AFB1 exposure induced an increase in H3K27me3 levels in EBV-infected cells, counteracting the initial decrease observed upon EBV infection. Additionally, changes in acetylation patterns of H4 N-tail residues and key regulatory proteins suggest potential disruptions in chromatin accessibility and transcriptional regulation. Correlation and network-based analyses further highlight coordinated epigenetic shifts in response to AFB1, with key hubs emerging within the histone code. Despite subtle differences, no significant divergence in overall hPTM responses was detected between EBV-infected and uninfected cells, emphasizing the complexity of epigenetic regulation under combined exposures. These findings provide valuable insights into the interplay between dietary carcinogens and viral infections, shedding light on potential mechanisms driving BL pathogenesis. Future research should explore locus-specific epigenetic changes and therapeutic interventions targeting hPTMs to mitigate cancer risk associated with AFB1 exposure and EBV infection.