Immunomodulation has made remarkable progress in fighting infectious disease and cancer. Conventionally, immunomodulation largely relies on chemical/biochemical agents, which, unfortunately, suffer from sever off-target adverse effects. Recent insights into nano-bio interactions suggest that nanomaterials can directly participate in immunomodulation. A range of physical and chemical cues at the nano-bio interface have been harnessed to regulate diverse immuno-signaling for disease control and treatment. In this Minireview, we summarize recent studies on the physical and chemical cues enabled by intrinsic nanomaterials to trigger immunological signaling. First, we discuss physical cues mediated by surface topography, hydrophobicity, charge, and heat at the nano-bio interface for immunomodulation. Then, various nanomaterials enabled chemical cues, such as metal species and oxidative species are outlined. Finally, our perspectives on challenges and possible future directions are provided.