Studies with fish larvae have reported poor performance associated with quantitative lipid imbalances in the diet and a lower dietary protein/neutral lipid ratio has been shown to result in an increased accumulation of lipid droplets in the enterocytes and in reduced fatty acid (FA) absorption efficiency in larval Senegalese sole. The present study examined the effect of dietary protein/neutral lipid ratios on amino acid (AA) absorption efficiency and metabolism, gut histology and growth in Senegalese sole larvae. Larvae were fed either non-enriched Artemia (NEA) or Artemia enriched on a soybean oil emulsion (EA) following larval settlement (at 16 days after hatching—DAH). AA absorption efficiency and metabolism were determined at 27 and 33 DAH by feeding the larvae on 14 C-AA-labeled Artemia. The effect on FA absorption was also verified at 28 DAH by tube feeding a lipid mixture containing the 14 C-labeled triacylglycerol triolein (TRI). A significantly lower growth was obtained with the EA diet, which also lead to an increased lipid accumulation in the gut epithelium. Feeding larvae with EA resulted in lower 14 C-FA absorption (significantly lower gut and body retention and higher label evacuation) at 28 DAH but no effect was noted in 14 C-AA absorption 24 h after feeding, at 27 and 33 DAH. However, larvae fed NEA evacuated a significantly higher amount of 14 C-AA at 3 h after feeding and presented a significantly higher AA catabolism. This indicates a faster AA absorption in NEA-fed larvae, which may allow more time for its metabolic use. On the other hand, a higher net AA absorption may be achieved in larvae fed NEA through a more rapid clearance of the lumen and sustained ingestion of the diet. The significantly higher growth of larvae fed NEA may thus be explained by a higher FA absorption efficiency and/or by an increased ingestion rate of a diet containing a lower lipid level.