Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477. Display omitted •Daily microbiome variation is related to food choices, but not to conventional nutrients•Daily microbiome variation depends on at least two days of dietary history•Similar foods have different effects on different people’s microbiomes Dietary intake is often considered to be a driver of microbiome variation. Johnson et al. use longitudinal sampling and daily dietary records to model microbiome changes in response to diet and find that microbiome responses to diet are personalized.