Comparisons among countries can help to identify opportunities for the reduction of inequalities in cardiometabolic health. The present cross-sectional analysis and meta-analysis aim to address to what extent obesity traits, socioeconomic, and behavioral factors determine poor metabolic health across body mass index (BMI) categories in two urban population-based samples from Central Europe. Data from the CoLaus (~6,000 participants; Lausanne, Switzerland) and the Kardiovize Brno 2030 (~2,000 participants; Brno, Czech Republic) cohorts. For each cohort, logistic regression analyses were performed to identify the main determinants of poor metabolic health overall and stratified by body mass index (BMI) categories. The results of each cohort were then combined in a meta-analysis. We first observed that waist circumference and body fat mass were associated with metabolic health, especially in non-obese individuals. Moreover, increasing age, being male, having low-medium educational level, abdominal obesity, and high body fat mass were the main determinants of the metabolically unhealthy profile in both cohorts. Meta-analysis stratified by BMI categories confirmed the previous results with slight differences across BMI categories. In fact, increasing age and being male were the main determinants of poor metabolic health independent of obesity status. In contrast, low educational level and current smoking were associated with poor metabolic health only in non-obese individuals. In line, public health strategies against obesity and related comorbidities should aim to improve social conditions and to promote healthy lifestyles before the progression of metabolic disorders.