Host circadian rhythmicity and the timing of feeding are increasingly recognized to cross-regulate and entrain each other, and may play crucial roles in regulating multiple physiological functions including host immunity and metabolic health. Of relevance, these circadian diet-immune interactions may be modulated by the gut microbiota. We review current knowledge linking the circadian clock and dietary timing to host immune-microbiota interactions, exemplifying how this axis may impact on host immunity in health and in a variety of immuneme-diated diseases. We also discuss current challenges in reaching mechanistic insights regarding the functions of the diurnally shifting diet-microbiome-host immune axis. We highlight the possible implications of circadian reprogramming by dietary timing patterns as a future intervention to modulate a variety of immune-related diseases.