Lysosome-rich enterocytes (LREs) are a specialized population of intestinal cells that mediate the uptake and absorption of dietary proteins in fish and neonatal mammals. Loss of LRE function causes inhibited growth and poor survival due to protein malnutrition. Previously, we reported that in zebrafish loss of Plasmolipin (pllp), an endosomal membrane protein highly expressed in LREs, impairs LRE differentiation and dietary protein absorption, resulting in marked reduction in survival rates. Raising pllp homozygous mutants surviving to adulthood and in-crossing them for multiple generations resulted in their adaptation to malnutrition, with adapted pllp mutants showing no survival deficits. To uncover mechanisms underlying this phenomenon, we compared the older adapted pllp allele with genetically related wild type (WT) fish and a newly generated pllp mutant allele. Using transcriptome profiling and quantitative protein absorption assays, we found that adapted pllp mutants exhibit upregulation of LRE endocytic components, resulting in a capacity for protein absorption that exceeds that of WT. This hyperactivation of LRE endocytic and absorptive activity is aided by a fine-tuned transcriptional regulation of immune genes that may contribute to the enhanced survival of pllp mutants in the face of increased exposure to environmental antigens. Genetic analyses indicate that these adaptations emerge gradually and are recurrent as shown experimentally by the adaptation of a mutant allele upon inbreeding and natural selection. Overall, our study illustrates that genome wide transcriptional changes underly adaptation mechanisms that enhance intestinal function and organismal survival in response to protein malnutrition.