Critical thinking is essential in academia and the workforce. Although writing can be used as a pedagogical tool for fostering deeper subject matter understanding, increased retention, and critical thinking, relatively few science courses are writing based. This writing-based introductory science course provided an opportunity for students to learn biology content through writing while also developing critical thinking skills. In this undergraduate introductory biology course, a learning progression framework was applied to writing assignments in order to promote critical thinking. Early course assignments focused on lower-order critical thinking, including information gathering and concept connecting activities, and served as the foundation for writing an evaluative research paper (REP) that required the application and analysis of biology content knowledge within different contexts. Based on the analysis of REP assignments using standardized criteria for assessing critical thinking, students were found to significantly increase their ability to demonstrate critical thinking. Students also became more aware of their critical thinking development, made stronger connections between concepts and applications in other contexts, and displayed measurable increases in critical thinking from their first to final drafts of their papers.