Aim Maternal diets introduce transcriptional changes in the offspring, highlighting the concept of genetic and physiological plasticity. Our previous analyses investigated stage‐dependent transcriptional responses to either maternal high or low protein:carbohydrate ratios in either muscle or liver. Fetal programming is proposed to be mediated by a small number of gatekeeper processes, such as cytoskeleton remodeling and cell cycle regulation. Here, we conducted an overall analysis of a three‐dimensional dataset aiming to elucidate, whether there are universally targeted pathways of adaptive transcriptional response to different protein:carbohydrate ratios. Methods Microarray analyses were performed on liver and skeletal muscle tissue sampled at 94 days post‐conception and 1, 28, and 188 days post‐natum from offspring (n=253) of German Landrace gilts that were fed isoenergetic diets containing low, high, or adequate protein. Results Cluster analyses revealed a hierarchical influence of tissue, ontogenetic stage, and diet on transcript levels. Considering results cumulatively over stages, liver showed only marginal transcriptional differences between the dietary groups, whereas considerable differences appeared in muscle. Considering results cumulatively over tissues, nutrition responsive transcriptions were observed along ontogenesis. Pathway analyses revealed transcript differences in genes related to tissue remodeling, cell cycle regulation, and mitochondrial function. Conclusion The factors tissue, stage, and diet impact gene expression in a hierarchical order. Porcine liver appeared to be a tissue that was more resilient to nutritional modulation compared to skeletal muscle tissue. In muscle, differential modulation between tissues and dietary groups reveal that there are no universal target‐pathways of adaptive transcriptional response to different protein diets. This article is protected by copyright. All rights reserved.