The use of modeling-based instruction is very effective when learning science content in multiple disciplines for native speakers. However, the benefits of using this pedagogy with students learning English as a second language or English Learners (ELs) have not been widespread, especially at the upper secondary level. This article discusses the use of a modeling-based natural selection unit that was developed for 14-16-year-old ELs in a sheltered EL biology class in the United States. The activity described for ELs includes not only activity details but also specifics about the inclusion and use of research-based scaffolding techniques. The efficacy of the unit was assessed in terms of changes to both conceptual understanding and scientific reasoning skills for the ELs and two inquiry-based non-EL biology classrooms. This modeling-based pedagogy allowed the ELs to not only increase their conceptual understanding of evolution but also their reasoning skills while also removing any knowledge gap with their non-EL peers in terms of evolution. The implication is that modeling-based science activities might hold the key to allowing EL students to achieve at the same conceptual levels as their non-EL peers.