It seems that during SARS-CoV-2 infection, total cholesterol, LDL-C, and HDL-C values decrease and lipids could play a fundamental role in viral replication. Moreover, it has been shown that SARS-CoV-2 infection could influence thyroid function. We performed a retrospective analysis of 118 hospitalized patients with COVID-19, comparing pre-infection lipid profile (53 patients) and thyroid-stimulating hormone (TSH) values (45 patients) to those measured on admission. Our aim was to evaluate whether SARS-CoV-2 infection could be involved in thyroid and lipid profile alterations and study possible correlations with disease severity and clinical outcome. Median baseline values at the admission time were: total cholesterol at 136.89 ± 42.73 mg/dL, LDL-C 81.53 ± 30.35 mg/dL, and HDL-C 32.36 ± 15.13 mg/dL; and triglycerides at 115.00 ± 40.45 mg/dL, non-HDL-C 104.53 ± 32.63 md/dL, and TSH 1.15 ± 1.08 μUI/mL. Median values of pre-infection total cholesterol, HDL-C, and TSH were significantly higher than those measured at the admission time (p value < 0.05). The C-reactive protein (CRP) negatively correlated with LDL-C (p = 0.013) and HDL-C (p = 0.05). Our data underline a possible impact of SARS-CoV-2 infection on thyroid function. Moreover it suggests a possible relation between COVID-19 and the lipid profile with a negative correlation between CRP, LDL-C, and HDL-C values, proposing the hypothesis that lipid lowering could follow the rising of the COVID-19 inflammatory state.