Introduction Diarrhea is a leading cause of child morbidity and mortality worldwide and is linked to early childhood stunting. Food contamination from improper preparation and hygiene practices is an important transmission pathway for exposure to enteric pathogens. Understanding the barriers and facilitators to hygienic food preparation can inform interventions to improve food hygiene. We explored food preparation and hygiene determinants including food-related handwashing habits, meal preparation, cooking practices, and food storage among caregivers of children under age two in Western Kenya. Methods We used the Capabilities, Opportunities, and Motivations model for Behavior Change (COM-B) framework in tool development and analysis. We conducted 24 focus group discussions with mothers (N = 12), fathers (N = 6), and grandmothers (N = 6); 29 key informant interviews with community stakeholders including implementing partners and religious and community leaders; and 24 household observations. We mapped the qualitative and observational data onto the COM-B framework to understand caregivers’ facilitators and barriers to food preparation and hygiene practices. Results Facilitators and barriers to food hygiene and preparation practices were found across the COM-B domains. Caregivers had the capability to wash their hands at critical times; wash, cook, and cover food; and clean and dry utensils. Barriers to food hygiene and preparation practices included lack of psychological capability, for instance, caregivers’ lack of knowledge of critical times for handwashing, lack of perceived importance of washing some foods before eating, and not knowing the risks of storing food for more than four hours without refrigerating and reheating. Other barriers were opportunity-related, including lack of resources (soap, water, firewood) and an enabling environment (monetary decision-making power, social support). Competing priorities, socio-cultural norms, religion, and time constraints due to work hindered the practice of optimal food hygiene and preparation behaviors. Conclusion Food hygiene is an underexplored, but potentially critical, behavior to mitigate fecal pathogen exposure for young children. Our study revealed several knowledge and opportunity barriers that could be integrated into interventions to enhance food hygiene.