Acetyl-CoA is a crucial metabolic intermediate at the intersection of nutrient catabolism, lipid biosynthesis, protein modifications, and regulation of gene expression. Dysregulated acetyl-CoA metabolism has been implicated in metabolic diseases, neurological disorders, and various types of cancer. Modulating two key acetyl-CoA producing enzymes, ATP-citrate lyase (ACLY) and acyl-CoA synthetase short chain family member 2 (ACSS2), has been demonstrated as a promising therapeutic strategy for cancer in preclinical models. However, it is critical to determine how systemic targeting of these ubiquitously expressed enzymes would interfere with normal tissue functions. Previous studies showed that constitutive ACSS2 knockout results in minimal phenotypes, but constitutive ACLY knockout is embryonic lethal in mice. In this study, we set out to determine the essential roles of ACLY in adult tissues and the toxicities that might occur upon systemic ACLY inhibition. To this end, we generated inducible whole-body Acly knockout mice and uncovered the indispensable role of ACLY in maintaining skin barrier integrity that cannot be fully compensated by ACSS2 upregulation. Further exhaustion of the acetyl-CoA pool by skin-specific double knockout (DKO) of Acly and Acss2 both exacerbates skin abnormalities and triggers severe weight loss and adipose tissue depletion. In the skin of DKO mice, we observed differential effects of acetyl-CoA deficiency on two major lipid producing compartments. While the epidermis is deprived of major lipids which are important for skin barrier function, the sebaceous glands unexpectedly increase lipid-rich sebum secretion despite impaired production of acetyl-CoA as a precursor for lipid synthesis. This excess sebum coincides with overexpression of thymic stromal lymphopoietin (TSLP), an epidermally-produced cytokine previously shown to stimulate sebum production that is linked to adipose tissue lipolysis. The data suggest that stored lipids in adipose depots are mobilized to support sebum production in acetyl-CoA deficient skin. Furthermore, dietary lipid supplementation partially improves skin conditions, lowers TSLP levels, and reduces adipose lipolysis in DKO mice. Together, the data establish the importance of skin intrinsic acetyl-CoA synthesis for barrier maintenance and reveal the skin as key determinant of systemic lipid partitioning.