Semen contain a heterogeneous population of viable and non-viable (damaged) spermatozoa. Proportions of non-viable spermatozoa interfere with male fertility, with available techniques unable to selectively remove prior to breeding. Nanobiotechnology may allow removal, enriching semen with high quality spermatozoa for improved productivity. Here, we applied double nanopurification with boar semen using functionalized magnetic nanoparticles. Non-viable and viable spermatozoa were magnetically separated and verified through various microscopy imaging. Viable (nanopurified) spermatozoa showed no additional damages. Nanopurification did not interfere with sperm motility and viability, with beneficial effects on motion parameters. Nanopurified spermatozoa maintained fertility following insemination, with resulting offspring indicating no impaired growth or health performance. Pork quality was unaffected showing comparable characteristics to the control. In summary, the use of magnetic nanopurification in boar spermatozoa showed sperm viability and fertility improvements with successful offspring performance. This study shows promise for large-scale commercial applications to enhance male fertility and offspring performance.