The consumption of sugar-containing beverages (SCB) has been associated with obesity although the evidence in preschool children is scarce. Cross-sectional analyses were performed to assess the association between obesity and SCB consumption (packaged juices and sugar-sweetened soft drinks) in 1823 children at the age of 4–5 years from the INfancia y Medio Ambiente (INMA) Project. One drink was defined as a glass of 175 mL, and the consumption of SCB was categorized in <1, 1–7 drinks/week and > 1 drink/day. We used multiple logistic regression to estimate odds ratios (OR). The average SCB consumption was 79.1 mL/day, mainly from packaged juices (80.9%). The SCB consumption was lower in non-obese children than in children with obesity, 76.6 vs 118.4 mL/day (p = 0.02). After adjusting for covariates, children who consumed >1 drink/day showed elevated odds of obesity, OR = 3.23 (95% confidence interval (CI): 1.48–6.98) compared to children who consumed <1 SCB drink a week. Each additional SCB drink per day was associated with higher odds of obesity, OR = 1.55 (1.14–2.09). Higher consumption of packaged juices, but not sugar-sweetened soft drinks, was significantly associated with higher odds of obesity, OR = 1.55 (1.09–2.15) and OR = 1.59 (0.76–3.39), respectively. A higher SCB consumption is associated with obesity in preschool children, mainly due to the consumption of packaged juices.