The jalapeño pepper is a vegetable of great economic importance worldwide. However, low germination efficiency, weak seedlings, and a high mortality rate during transplant compromise the viability and sustainability of the crop. An innovative solution is the nanopriming technique, an emerging and novel technology, which involves the imbibition of seeds for a specific period using mineral nanoparticles. The addition of micronutrients such as zinc and molybdenum has been used in seed germination and early seedling development due to their crucial roles. The aim of this study was to evaluate the effectiveness of using zinc–molybdenum nanopriming in jalapeño pepper on germination and early growth. The results showed that applying nanopriming (124–10 mg L−1 of zinc–molybdenum) promotes the effectiveness on the imbibition and germination of jalapeño pepper seeds, resulting in heavier seeds with a better initial absorption. This method not only improves germination rates and seedling vigor, but also points towards more sustainable and efficient agriculture. Building on these findings, the zinc–molybdenum nanopriming method could potentially transform jalapeño pepper cultivation by enhancing seed quality and resilience. Nanopriming could help increase crop yields and minimize reliance on chemical inputs, such as fertilizers and pesticides, which might reduce production costs and environmental impact.