Little research exists on effective ways to prepare secondary mathematics and science teachers to work with English language learners (ELLs) in mainstream mathematics and science (subsequently referred to as STEM) classrooms. Given the achievement gap that exists between ELLs and their native-speaking counterparts in STEM subjects, as well as the growing numbers of ELLs in US schools, this becomes a critical issue, as academic success for these students depends on the effectiveness of instruction they receive not only in English as a second language classes (ESL), but in mainstream classrooms as well. This article reports on the effects of a program restructuring that implemented coursework specifically designed to prepare pre-service and in-service mathematics, science, and ESL teachers to work with ELLs in their content and ESL classrooms through collaboration between mainstream STEM and ESL teachers, as well as effective content and language integration. We present findings on teachers' attitudes and current practices related to the inclusion of ELLs in the secondary-level content classroom and their current level of knowledge and skills in collaborative practice. We further describe the rationale behind the development of the course, provide a description of the course and its requirements as they changed throughout its implementation during two semesters, and present findings from the participants enrolled. Additionally, we discuss the lessons learned; researchers' innovative approaches to implementation of content-based instruction (CBI) and teacher collaboration, which we term two-way CBI (DelliCarpini & Alonso, 2013); and implications for teacher education programs.