Upwelling oceanographic phenomenon is associated with increased food availability, low seawater temperature and pH. These conditions could significantly affect food quality and, in consequence, the growth of marine species. One of the most important organismal traits is somatic growth, which is highly related to skeletal muscle. In fish, skeletal muscle growth is highly influenced by environmental factors (i.e. temperature and nutrient availability) that showed differences between upwelling and downwelling zones. Nevertheless, there are no available field studies regarding the impact of those conditions on fish muscle physiology. This work aimed to evaluate the muscle fibers size, protein content, gene expression of growth and atrophy-related genes in fish sampled from upwelling and downwelling zones. Seawater and fish food items (seaweeds) samples were collected from upwelling and downwelling zones to determine the habitat's physical-chemical variations and the abundance of biomolecules in seaweed tissue. In addition, white skeletal muscle samples were collected from an intertidal fish to analyze muscular histology, the growth pathways of protein kinase B and the extracellular signal-regulated kinase; and the gene expression of growth- (insulin-like growth factor 1 and myosin heavy-chain) and atrophy-related genes (F-box only protein 32 and muscle RING-finger protein-1). Upwelling zones revealed higher nutrients in seawater and higher protein content in seaweed than samples from downwelling zones. Moreover, fish from upwelling zones presented a greater size of muscle fibers and protein content compared to downwelling fish, associated with lower protein ubiquitination and gene expression of F-box only protein 32. Our data indicate an attenuated use of proteins as energy source in upwelling conditions favoring protein synthesis and muscle growth. This report shed lights of how oceanographic conditions may modulate food quality and fish muscle physiology in an integrated way, with high implications for marine conservation and sustainable fisheries management.