The impact of alcohol on the body can be investigated with NMR spectroscopy in vitro, which can detect a wide range of metabolites but preparing samples includes tissue biopsy. Blood sampling is less invasive, but blood metabolic content might not reflect the changes occurring in other tissues. Thus, this study aimed to investigate the liver, brain, and serum metabolism and evaluate the link between tissues and serum metabolic content. Two experimental groups with ten outbred rats each were provided intragastrically with water (control group) and 50% ethanol solution (alcohol group) for 28 days. 1H NMR spectroscopy in vitro was performed on the brain cortex, liver, and serum samples. Student’s t test with Holm–Bonferroni correction was used to investigate significant differences between groups. Partial least-squares discriminant analysis (PLS-DA) and two-way ANOVA were performed to compare liver and serum, brain and serum. In all, 38, 37, and 21 metabolites were identified in the liver, brain, and serum samples, respectively. Significant differences for three metabolites were found in the liver (alanine, proline, and glutathione, p < 0.002) and four in serum (lactate, betaine, acetate, and formic acid, p < 0.002) were detected between the control and alcohol groups. The contents of glucose, betaine, and isoleucine were correlated (r > 0.65) between serum and liver samples. PLS-DA determined separation between all tissues (p < 0.001) and between control and alcohol groups only for liver and serum (p < 0.001). Alcohol had a more substantial effect on liver and serum metabolism than on the brain.