Endocrine-disrupting chemicals can induce metabolic alterations, resulting in diseases such as obesity, diabetes, and fatty liver disease, which can be inherited by offspring inhabiting uncontaminated environments. Bisphenol A (BPA), a well-known endocrine disruptor, can induce endocrine disruption, leading to metabolic disorders in subsequent generations without further exposure to BPA via nongenetic transgenerational inheritance. Using medaka as an animal model, we reported that ancestral BPA exposure leads to transgenerational nonalcoholic fatty liver disease (NAFLD) in grandchildren four generations after the initial exposure. It is unclear if transgenerational NAFLD developed because ancestral BPA exposure differs from that developed due to direct and continuous BPA exposure because the transgenerational disease develops in the absence of the stressor. We induced transgenerational NAFLD in medaka with ancestral BPA exposure (10 µg/L) at the F0 generation and examined transcriptional and metabolomic alterations in the liver of the F4 generation fish that continued to develop NAFLD. To understand the etiology of NAFLD in unexposed generations, we performed nontargeted liquid chromatography-mass spectrometry-based metabolomic analysis in combination with bulk RNA sequencing and determined biomarkers, co-expressed gene networks, and sex-specific pathways triggered in the liver. An integrated analysis of metabolomic and transcriptional alterations revealed a positive association with the severity of the NAFLD disease phenotype. Females showed increased NAFLD severity and had metabolic disruption involving proline metabolism, tryptophan metabolism, and bile metabolism pathways. The present results provide the transcriptional and metabolomic underpinning of metabolic disruption caused by ancestral BPA exposure, providing avenues for further research to understand the development and progression of transgenerational NAFLD caused by ancestral bisphenol A exposure.