The use of scientific modeling has been shown to be highly effective in the learning of science content in multiple disciplines for non-English Learners (EL). However, the benefits of using this pedagogy with ELs have not been heavily explored. This article discusses the use of modeling-based evolution and population ecology pedagogical units in a sheltered biology high school class for ELs. A sheltered EL class is one where only ELs are enrolled and they learn both language and science concurrently. This article specifies the at the scaffolding used to adjust the pedagogy for this unique set of students. The effectiveness of this method was assessed using a convergent mixed method case study design. Data was collected using assessments in content, scientific reasoning and attitudes towards science (i.e., self-efficacy, fascination, and valuation of science) as well as teacher interviews, and classroom observations. The cases were an EL modeling-based sheltered biology class, and two non-EL inquiry-based biology classes, all at the upper secondary level. The EL modeling cohort achieved posttest comparison content scores that were not significantly different from the non-EL cohort and significantly higher posttest scientific reasoning scores. The effect sizes in both of these cases were much larger for the EL cohort. The affective assessments demonstrated intriguing results with the EL cohort having a greater fascination with science than the non-EL cohort but a decline in self-efficacy. Both cohorts valued science to the same extent. This methodology holds promise in helping to decrease the science gap between ELs and non-ELs taught with inquiry-based pedagogies.