Background: Betaine, an osmolyte derivative of the metabolite choline and the amino acid glycine, acts as a methyl donor in the conversion of homocysteine to methionine and is involved in the maintenance of adequate lipid metabolism. There is growing evidence for the role of betaine in the development of various lipid-related diseases, including dyslipidemia and cardiovascular risk. This study aimed to analyze associations between betaine intake and blood lipid profiles in Mexican subjects. Methods: A total of 212 adults were randomly recruited in the city of Tijuana, Baja California, Mexico. Betaine intake was estimated using Nutritionist Pro software. Body composition and metabolic measurements were obtained by conventional methods. In the total sample, the average intake of betaine was 14.32 mg/d. Individuals were categorized into three groups according to tertiles of betaine consumption: tertile/group 1 (<4.16 mg/d), tertile/group 2 (4.16–12.02 mg/d), and tertile/group 3 (>12.02 mg/d). Results: Compared to group 3, subjects within group 1 had higher serum levels of total cholesterol (p = 0.001), LDL-c (p = 0.026), and non-HDL-c (p = 0.021). In addition, significant negative Pearson correlations were found between betaine intake and the serum levels of total cholesterol (r = −0.432, 95% CI, −0.684, −0.185, p = 0.001), LDL-c (r = −0.370, 95% CI, −0.606, −0.134, p = 0.002), and non-HDL-c (r = −0.351, 95%CI, −0.604, −0.098, p = 0.007). Conclusions: Our results show that a low intake of betaine is associated with elevated blood cholesterol levels in Mexican subjects. On this basis, betaine consumption could be used as an additional dietary measure for cardiovascular care. However, additional studies are required to confirm our results in other Mexican regions as well as in other populations worldwide.