Standard extended semen contains both viable and non-viable spermatozoa. Magnetic nanoparticles have proven to be effective in the purification of boar semen by targeting nonviable spermatozoal cells (Feugang et al. 2015 IVF Reprod. Med. Genet. 3, 2), allowing potentially greater efficiency within the pork production industry. Previous research lacks data regarding the biochemical effects on offspring produced from such nanopurified semen. Here, we aim to determine whether there is a difference in protein expression between offspring produced with standard and nanopurified semen. Myoglobin (MYO) and fatty acid synthase (FAS) were chosen as the protein markers for this study because they are often studied in reference to meat quality. Myoglobin provides meat its red colour, and FAS assembles fatty acids contributing to tenderness and palatability. The results produced here will provide a baseline for further research in the meat quality and the safety of consuming meat produced with this nanopurification method. Six sows maintained on our experimental farm were inseminated with standard (CTRL) and nanopurified (NANO) boar semen, leading to the birth of viable full-term piglets. At weaning, 10 pigs (5 male and 5 female) were randomly selected from each group and allowed to grow to market weight. Samples of longissimus muscle and SC back fat were then collected from each pig and prepared for protein analyses. Western immunoblotting and immunofluorescence of tissue samples were performed using anti-MYO and anti-FAS antibodies. Images were appropriately captured and quantified (ImageJ). Data (mean ± SEM) were analysed (ANOVA/Wilcoxon) with P < 0.05 set as threshold of significance. Western immunoblotting confirmed the specificity of each antibody. Myoglobin and FAS proteins were highly detected in muscle and fat tissues, respectively, and there were no differences between groups for each protein. Compared with the CTRL group, immunofluorescence signals of MYO in fat tissues and FAS in muscle tissues were significantly reduced in NANO group pigs, irrespective of the sex. However, MYO immunofluorescence levels in fat tissues and FAS levels in all tissues were significantly reduced in females of the NANO group compared with their counterparts in the CTRL group. In conclusion, MYO and FAS proteins were confirmed as good markers for muscle and fat tissues, respectively, with similar immunofluorescence levels between CTRL and NANO groups. Current preliminary data also show that sperm nanopurification (1) may decrease FAS protein expression in muscle tissue with the possibility to affect meat quality and (2) mainly affected females in this study. Further studies are needed for confirmation of these early findings.