Ischemia-reperfusion injury is a common complication during liver surgery, where steatotic livers are more prone to the injury and may become more prevalent in the growing obese population. This study aimed to characterize liver morphology and understand changes in subcellular function in steatotic livers exposed to ischemia-reperfusion injury through quantitative description of fluorescein distribution obtained by minimally-invasive in vivo multiphoton microscopy using a physiological pharmacokinetic model. Rats were fed a high fat diet for 7 days to induce liver steatosis. Partial ischemia was induced, following reperfusion for 4 hours, when fluorescein (10 mg/kg) was injected intravenously. Liver images, bile and blood were collected up to 180 min following injection. Ischemia-reperfusion injury was associated with an increase in alanine transaminase levels and apoptosis. In addition, steatosis had the presence of lipid droplets and an increase in the fluorescein associated fluorescence observed in the hepatocytes by multiphoton imaging. Analysis of the hepatic concentration-time profiles suggests that the steatosis induced increase in fluorescein associated fluorescence mainly arises by inducing the hepatic fluorescein metabolism. The combination of ischemia-reperfusion with steatosis exacerbates these effects further. This was confirmed by fluorescence lifetime imaging microscopy showing a decreased average fluorescence lifetime of the liver, indicative of increased production of the metabolite. Our results show the potential of non-invasive imaging of a dye to further improve our understanding of liver disease induced subcellular changes in vivo by also providing further quantitative measures of metabolic and biliary liver function and, hence, extending the qualitative liver function tests now available.