The effect of feed restriction on the liver protein profiles of two different breeds of sheep was studied. We compared Merino with the Damara, breeds with respectively low and high tolerance to nutritional stress. Each breed was grouped into two nutritional treatments: restricted (12–14% loss of live weight) and control (maintenance). The trial lasted 42 days. Animals were sacrificed and liver samples subjected to label free shotgun proteomics. The resultant proteins had both their fold change and statistical significance in an unpaired t-test calculated to identify differential protein abundance. The tool WebGestalt was utilized to perform an Overrepresentation Enrichment Analysis (ORA) for gene ontology terms associated with the significant proteins. We further validated shotgun proteomics findings using a selected reaction monitoring (SRM)-based targeted proteomics approach, where similar trends in regulation were obtained for a subset of relevant proteins across an independent cohort of animals. Results confirm that Damara has adapted to nutritional stress by mobilizing stored fatty acids within adipose tissue and converting them to energy more efficiently than Merino. Finally, Merino had an overabundance pattern primarily directed to protein synthesis pathways. Regulated proteins identified may be used as a basis for marker selection towards tolerance to nutritional stress. Biological significance: Sheep are one of the most important livestock animals. They remain however poorly understudied and described. Seasonal weight loss (SWL) due to pasture scarcity during the dry season is one of the most limiting conditions to ruminant production in the tropics. To counter SWL, farmers may use supplementation, expensive or difficult to implement. A more suitable long-term solution would be to use breeds that are naturally adapted to nutritional stress. This work contrasts two breeds with different levels of tolerance to SWL, the Damara and the Merino, respectively well and poorly adapted. Comparison is conducted at the level of the hepatic tissue and using label free proteomics. This work identifies a series of pathways in the liver of the Damara via label free proteomics that suggest a unique fatty acid metabolic process within this breed. Proteins that have increased abundance in the Damara in association with fatty acid metabolism may be used as potential markers of tolerance to nutritional stress. This research will pave the way for more viable, long-term solutions for farmers facing annual production problems due to drought in the tropics and the Mediterranean region.