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Chronic disruption of the synchronous relationship between endogenous and exogenous circadian timing is associated with the development of obesity and metabolic disease. Social jetlag is a measure of circadian misalignment and has been identified as a risk factor for overweight and related diseases. However, the mechanisms involved in this relationship remain underexplored. The objective of this study was to investigate the association between social jetlag and food consumption at late meal timing in patients with obesity-related chronic diseases. This study included 792 individuals (73% female; age 55.9 ± 12.4 years) in which the prevalence of social jetlag (>1h) was 24.4% (n = 194). Participants with social jetlag reported late meal timing for breakfast, early afternoon snack and dinner. Individuals with social jetlag also reported a higher intake of total calories (kcal), protein, total fat, saturated fat, cholesterol, and servings of meat and eggs and sweets in relation to those without social jetlag. Regarding the consumption during each meal of the day, participants with social jetlag had consumed more calories, saturated fat and cholesterol during dinner; more protein, total fat, saturated fat, and cholesterol during lunch; and more total fat and saturated fat during morning snack. In addition, individuals with social jetlag had a higher risk of inadequate consumption of total fat, saturated fat and cholesterol intake when compared with those without social jetlag. We conclude that social jetlag is associated with a poor diet and later meal times, which should be avoided in individuals with obesity-related chronic diseases. More studies are needed to confirm these findings.