Dietary intervention is a key strategy for preventing and managing chronic kidney disease (CKD). However, evidence on specific foods’ effects on CKD is limited. This study aims to clarify the impact of various foods on CKD risk. We used two-sample Mendelian randomisation to analyse the causal relationships between the intake of eighteen foods (e.g., cheese, processed meat, poultry, beef and non-oily fish) and CKD risk, as well as estimated glomerular filtration rate (eGFR)cr and eGFRcys levels. The inverse variance weighting method, weighted median method, MR-Egger regression, simple mode and weighted mode were employed. The sensitivity analysis included Cochran’s Q test and the Egger intercept test. According to the main method, the IVM results indicated that frequent alcohol intake was linked to higher CKD risk (P= 0·007, 0·048). Protective factors included cheese (OR = 0·71, (95 % CI: 0·53, 0·94), P= 0·017), tea (OR = 0·66, (95 % CI: 0·43, 1·00), P= 0·048) and dried fruit (OR = 0·78, (95 % CI: 0·63, 0·98), P= 0·033). Oily fish (β = 0·051, (95 % CI: 0·001, 0·102), P= 0·046) and dried fruit (β = 0·082, (95 % CI: 0·016, 0·149), P= 0·014) were associated with elevated eGFRcys. Salad/raw vegetables (β = 0·024, (95 % CI: 0·003, 0·045), P= 0·028) and dried fruit (β = 0·013, (95 % CI: 0·001, 0·031), P= 0·014) were linked to higher eGFRcr, while cereal intake (β = –0·021, (95 % CI: −0·033, −0·010), P < 0·001) was associated with lower eGFRcr. These findings provide insights for optimising dietary strategies for CKD patients.