Science graduates require critical thinking skills to deal with the complex problems they will face in their 21st century workplaces. Inquiry-based curricula can provide students with the opportunities to develop such critical thinking skills; however, evidence suggests that an inappropriate level of autonomy provided to underprepared students may not only be daunting to students but also detrimental to their learning. After a major review of the Bachelor of Science, we developed, implemented, and evaluated a series of three vertically integrated courses with inquiry-style laboratory practicals for early-stage undergraduate students in biomedical science. These practical curricula were designed so that students would work with increasing autonomy and ownership of their research projects to develop increasingly advanced scientific thinking and communication skills. Students undertaking the first iteration of these three vertically integrated courses reported learning gains in course content as well as skills in scientific writing, hypothesis construction, experimental design, data analysis, and interpreting results. Students also demonstrated increasing skills in both hypothesis formulation and communication of findings as a result of participating in the inquiry-based curricula and completing the associated practical assessment tasks. Here, we report the specific aspects of the curricula that students reported as having the greatest impact on their learning and the particular elements of hypothesis formulation and communication of findings that were more challenging for students to master. These findings provide important implications for science educators concerned with designing curricula to promote scientific thinking and communication skills alongside content acquisition.