ABSTRACT Objective To verify the multivariate relationships between eating habits, cardiorespiratory fitness, body mass index, and cardiometabolic risk factors in children. Methods This is a cross-sectional study developed in a public elementary school with 60 first- to sixth-graders. Their eating habits were assessed using the Food Frequency Survey, weight, height, and cardiorespiratory fitness, assessed according to the Projeto Esporte Brasil protocol. Moreover, the variables, high-density lipoprotein, low-density lipoprotein, glucose, insulin, C-reactive protein, adiponectin, leptin, diastolic and systolic blood pressure were evaluated. Descriptive statistics were used for data analysis and generalized estimation equations were used for the analysis of direct and indirect relations, in a multivariate analysis model with several simultaneous outcomes. Results It appears that the eating habits and cardiorespiratory fitness explain 20% of the body mass index. Cardiometabolic risk factors are explained by the relationship between eating habits, cardiorespiratory fitness, and body mass index, according to the following percentages: 29% (systolic blood pressure), 18% (diastolic blood pressure), 63% (leptin), 4% (adiponectin), 14% (C-reactive protein), 17% (insulin), 10% (high-density lipoprotein), 1% (low-density lipoprotein), 4% (glucose). It is also observed that the effects of the eating habits on cardiometabolic risk factors are indirect, that is, they are dependent on changes in the body mass index and cardiorespiratory fitness levels. Conclusions The relationship between eating habits and cardiometabolic risk factors in children is dependent on cardiorespiratory fitness and body mass index. Thus, our findings suggest a multivariate relationship between these factors.