Early initiation of breastfeeding (EIBF), exclusive breastfeeding (EBF), and minimum dietary diversity (MDD) are recommended infant and young child feeding (IYCF) practices. Subnational analyses of predictors of these practices are rare but can contribute to programmatic and policy decisions. The aim of this study was to assess predictors of EIBF, EBF, and MDD in Kaduna and Lagos States, Nigeria. This analysis of the population-based data from the Alive & Thrive impact evaluation [Kaduna (N = 4,702), Lagos (N = 1,563)] used chi-square automatic interaction detection to select variables related to EIBF, EBF, and MDD with P < 0.20. Final logistic regression models retained predictors associated with each outcome at P < 0.05. Positive predictors of EIBF were woman-headed household (both states), contact with a health worker (both), EIBF knowledge (both), EIBF awareness (Lagos), EIBF beliefs (both), EIBF self-efficacy (Kaduna), maternal education (Kaduna), household food security (Kaduna), delivery at health facility (Kaduna), counseling on EIBF (Lagos), and vaginal birth (Lagos). Maternal employment was negatively associated with EIBF (Kaduna). Positive predictors of EBF were EBF knowledge (both), EBF awareness (Kaduna), EBF beliefs (Kaduna), EBF self-efficacy (both), postpartum practices such as checking to see if the baby was sucking well (Kaduna), maternal education (Kaduna), household food security (Kaduna), and EBF norms (Lagos). The child having fever in the last 2 weeks was negatively associated with EBF (Kaduna). Positive predictors of MDD were child's age (both), socioeconomic status (both), four or more antenatal care visits (Kaduna), child still breastfed (Kaduna), complementary feeding awareness (Kaduna), complementary feeding beliefs (Kaduna), help from husband or mother/mother-in-law (Kaduna), contact with a health worker (Lagos), complementary feeding knowledge (Lagos), and complementary feeding self-efficacy (Lagos). Maternal education (Kaduna) and household food security (Lagos) were negatively associated with MDD. This study reveals that different combinations of behavioral factors and maternal and household characteristics are critical predictors of IYCF in Nigeria, though variations exist between Kaduna and Lagos. These insights can inform tailored state-specific IYCF interventions and policies to improve IYCF practices in Nigeria.