Menopause is often accompanied by visceral obesity. With the aim of exploring the consequences of ovarian failure on visceral fat, we evaluated the effects of ovariectomy and estrogen replacement on the proteome/phosphoproteome and on the fatty acids profile of the retroperitoneal adipose depot (RAT) of rats. Eighteen three months old female Wistar rats were either ovariectomized or sham-operated and fed with standard chow for three months. A sub-group of ovariectomized rats received estradiol replacement. RAT samples were analyzed using data-independent acquisitions LC-MS/MS and pathway analysis was performed with the differentially expressed/phosphorylated proteins. RAT lipid profile was analyzed by gas chromatography. Ovariectomy induced high adiposity and insulin resistance and promoted alterations in protein expression and phosphorylation. Pathway analysis showed that 5 pathways were significantly affected by ovariectomy, namely metabolism of lipids (included fatty acid metabolism and mitochondrial fatty acid β-oxidation), fatty acyl-CoA biosynthesis, innate immune system (included neutrophil degranulation), metabolism of vitamins and cofactors, and integration of energy metabolism (included ChREBP activates metabolic gene expression). Lipid profile analysis showed increased palmitic and palmitoleic acids content. The analysis of the data indicated that ovariectomy favored lipogenesis while it impaired fatty acids oxidation, and induced a pro-inflammatory state in the visceral adipose tissue. These effects are consistent with the findings of high adiposity, hyperleptinemia, and impaired insulin sensitivity. The observed alterations were partially attenuated by estradiol replacement. The data point to a role of disrupted lipid metabolism in adipose tissue in the genesis of obesity after menopause.