The advantages of active learning approaches have prompted national recommendations for the development of inquiry-based laboratories to replace traditional laboratory classes. However, there is little consensus for the most-effective implementation strategies. Frequently, a single inquiry-based exercise is incorporated at the end of a traditional course and students have little opportunity to repeat the experience before moving on to new courses. To test whether multiple-rounds of inquiry would be beneficial, we incorporated three rounds of inquiry-based experiments during a redesign of a traditional upper-level undergraduate developmental biology laboratory class. After the second and third round of inquiry, students gave slideshow presentations of their projects and received peer and instructor feedback. We then designed and validated a scoring rubric to assess student use of scientific skills. Substantial improvements were observed in five of seven categories of scientific skills when comparing student performance from the third round of projects to the second round. Surprisingly, these gains were not diminished when students in the course were given the rubric to use as a guide. Anecdotal evidence and responses to student questionnaires revealed substantial levels of student interest and engagement in the course. Overall, these results indicate that incorporating iterative rounds of inquiry-based laboratories is a promising strategy for teaching scientific skills, enhancing student engagement, and promoting learning.