The “gut–muscle axis” is an emerging concept that describes how intestinal microbiota influence skeletal muscle biology, especially energy metabolism. This biological communication is crucial for muscle development and directly affects meat production traits. Although the gut microbiota is known to modulate host metabolism, the specific molecular mechanisms by which diet shapes the gut–muscle axis are not well defined. This study aimed to use a network-based approach to dissect how dietary lipid sources—canola (CO) vs. soybean (SO) oil—can modulate the interaction between cecal microbiota and muscle transcriptome in pigs. Longissimus lumborum muscle (RNAseq) and cecal content (16S rRNA sequencing) samples were collected from 32 pigs fed diets supplemented with either 3% CO (N = 14) or 3% SO (N = 18). An analysis of the cecal microbiota yielded 447 core amplicon sequence variants (ASVs, 50% prevalence) but revealed no differences in community diversity between diets. In contrast, the muscle gene expression was distinctly clustered by diet. This prompted a diet-specific Weighted Gene Co-expression Network Analysis (WGCNA) to map interactions with the 19 most abundant (> 1% mean abundance) cecal genera. WGCNA yielded 41 gene modules for CO and 27 for SO. We found four relevant modules (|r|>0.7, p<0.01) for CO, positively correlated with the Rikenellaceae RC9 gut group and Leyella and negatively correlated with Akkermansia, Terrisporobacter, and Romboutsia. In the SO group, the two relevant modules were positively correlated with Prevotellaceae UCG-003 and Terrisporobacter. Our findings demonstrate that dietary fat sources reshape functional communication rather than the composition of the gut–muscle axis. The opposing association of Terrisporobacter, a genus linked to SCFA production, oxidative stress, and immunity, suggests that the fat source can influence metabolic and immune signaling in muscle. This integrative framework offers a powerful tool for the sustainable development of targeted nutritional strategies to enhance muscle development and pork quality.