Manganese is an important co-factor for numerous biological processes, including defense against reactive oxygen species. A common genetic variant in the manganese transporter SLC39A8 (p.Ala391Thr) has been associated with lower blood levels of manganese and with increases in markers of liver cell damage. Whether the variant confers an increased risk of liver disease is unclear. We tested the association of this variant with biochemical, imaging, and clinical hepatic traits and outcomes in large general population cohorts totaling up to one million individuals, including 991 cases with hepatocellular carcinoma (HCC) and 7,191 with cirrhosis. We found that the Thr-allele of p.Ala391Thr was associated with slightly higher plasma alanine transaminase and aspartate transaminase, markedly higher corrected T1 on hepatic magnetic resonance imaging (MRI), a presumed marker of liver inflammation, and with lower hepatic computed tomography attenuation. However, the variant was not associated with hepatic fat content, nor with the risk of HCC or cirrhosis. In conclusion, SLC39A8 p.Ala391Thr is associated with biochemical and imaging markers of hepatic inflammation, but the variant does not confer a higher risk of chronic liver disease. We hypothesize that the associations with hepatic imaging traits are due to lower hepatic manganese levels in carriers of the variant.