Background Colorectal cancer (CRC) has been reported as the third most commonly diagnosed cancer worldwide and is currently considered as a major public health concern. A peak increase in incidence has been noted in economically transitioning countries like Morocco where industrialization started shifting from a traditional lifestyle and diet toward a more westernized diet and lifestyle. Objective This paper aims to present the protocol of a large-scale Moroccan case-control study that aims at investigating associations of diet, other lifestyle factors, and genetic traits with CRC risk in Morocco. Methods A case-control study was conducted between 2009 and 2017, including 3032 case-control pairs (1516 cases and 1516 controls) matched on sex, age, and center in 5 major public health hospitals in Morocco. Questionnaires on sociodemographic data, lifestyle, family history of CRC, and nonsteroidal anti-inflammatory drugs (NSAIDs) were completed by trained investigators during face-to-face interviews. In addition, participants completed a semiquantitative food-frequency questionnaire, developed to assess food intake in the Moroccan population. Information regarding genetic factors was recorded for cases, and paraffin blocks (with embedded tumor tissues) are available in 3 collaborating hospitals. Conditional logistic regression analysis is planned to assess associations between diet and CRC risk. Binary logistic regression is considered to predict associations between mutations and nutritional risk factors including only CRC case series. Results Altogether, 2966 cases-control pairs (1483 cases and 1483 controls) were considered eligible and included in this study. Both cases and controls did not differ significantly with respect to age (P=.36), sex (P=.51), center (P>.99), marital status (P=.30), and NSAID use (P=.08). However, participants in the control group were significantly more likely to have a high income level and live in urban areas and to have a high level of education than cases. Conclusions This is the first study investigating potential risk factors of CRC such as lifestyle, diet, and genetic factors, originating from a southern Mediterranean country with low but increasing CRC prevalence. Identified risk factors allow the establishment of evidence-based preventive actions regarding nutrition and other lifestyle habits adapted to the Moroccan context. In brief, this study will promote cancer research and prevention in Morocco. International Registered Report Identifier (IRRID) RR1-10.2196/13998