Writing in science can be challenging for all learners, and it is especially so for students with cognitive or language-based learning difficulties. We examined the effects of a cognitive apprenticeship on student disciplinary writing skills as well as near and far transfer of learning outcomes. This instructional approach included a gradual release of responsibility for learning through four, 3-day investigations that included authentic scientific experiments, small- and whole-group discussions, and the construction and revision of scientific arguments. Intervention students showed significant gains for both near (effect size = 1.08) and far (effect size = 0.76) transfer disciplinary writing outcomes. These results held true even when compared with a nonequivalent control group (effect size = 1.95). Students with disabilities demonstrated similar rates of growth as peers without disabilities, especially with respect to the quality of their claims and ability to provide scientific evidence. This study provides additional data on the value of cognitive apprenticeships in middle school science classrooms, and the results indicate the importance of discussion in helping students to think and write more like scientists.