The aim of the present study was to compare biomarkers of one-carbon metabolism (OCM), lipid metabolism, and fatty liver in people with normal and increased body weight. The study was performed on 421 participants, aged 20–40 years, enrolled in Poznan, Poland, in 2016–2018. Choline and betaine intakes were assessed. DNA samples were genotyped for polymorphisms of phosphatidylethanolamine N-methyltransferase (<i>PEMT</i>; rs7946 and rs12325817), methylene tetrahydrofolate reductase (<i>MTHFR</i>; rs180113), methylenetetrahydrofolate dehydrogenase (<i>MTHFD1</i>; rs2236225), and dihydrofolate reductase (<i>DHFR</i>; rs70991108). To assess the associations between blood metabolites (choline, betaine, folate, L-carnitine, o-acetyl-L-carnitine, and trimethylamine N-oxide]), circulating lipids, and fatty liver indices, multiple logistic regression analyses were performed. Overweight/obese participants had 5.8% higher choline (<i>p</i> < 0.05) and 10% higher L-carnitine (<i>p</i> < 0.001) levels than normal-weight subjects. Serum folate and betaine levels were associated with lower total cholesterol (<i>p</i> < 0.001 and <i>p</i> < 0.05), low-density lipoprotein (LDL) cholesterol (<i>p</i> < 0.001 and <i>p</i> < 0.05, respectively), triacylglycerols (<i>p</i> < 0.01 and <i>p</i> < 0.001), and triglyceride glucose index (<i>p</i> < 0.001 and <i>p</i> < 0.01, respectively), though only in overweight/obese people. The <i>PEMT</i> rs12325817 CC genotype was associated with higher levels of high-density lipoprotein (HDL) cholesterol (<i>p</i> < 0.01) in overweight/obese people. The associations between OCM markers, fatty liver indices, and blood lipids differ in subjects with normal and excessive body weight.