Liver fibrosis is a strong predictor of long-term mortality in individuals with metabolic-associated fatty liver disease; yet, the mechanisms underlying the progression from the comparatively benign fatty liver state to advanced non-alcoholic steatohepatitis (NASH) and liver fibrosis are incompletely understood. Using cell-type-resolved genomics, we show that comprehensive alterations in hepatocyte genomic and transcriptional settings during NASH progression, led to a loss of hepatocyte identity. The hepatocyte reprogramming was under tight cooperative control of a network of fibrosis-activated transcription factors, as exemplified by the transcription factor Elf-3 (ELF3) and zinc finger protein GLIS2 (GLIS2). Indeed, ELF3- and GLIS2-controlled fibrosis-dependent hepatokine genes targeting disease-associated hepatic stellate cell gene programs. Thus, interconnected transcription factor networks not only promoted hepatocyte dysfunction but also directed the intra-hepatic crosstalk necessary for NASH and fibrosis progression, implying that molecular “hub-centered” targeting strategies are superior to existing mono-target approaches as currently used in NASH therapy. Display omitted •Advanced NASH is accompanied by partial loss of hepatocyte identity•NASH-induced hepatokines associate with fibrosis-linked genes in hepatic stellate cells•A cooperative transcription factor network drives hepatocyte genomic reprogramming in NASH•Fibrosis-activated ELF3 and GLIS2 promote intra-hepatic crosstalk and liver fibrosis The mechanisms that drive the advanced stages of metabolic-associated fatty liver disease (MALFD) are still largely unknown. Using a cell type-resolved genomics approach, Loft et al. identified a fibrosis-activated hepatocyte transcription factor network that contributes to the loss of hepatocyte identity and dictates intra-hepatic cross-talk during the progression of MALFD.