Due to inherent shortcomings in the traditional laboratory structure, inquiry-based laboratories have increasingly been adopted to increase student engagement in science and provide an early research experience. At Baylor University, a new inquiry-based introductory biology laboratory, the Ciliate Investigative Learning Initiative Classroom-Based Undergraduate Research Experience (CILI-CURE), has been designed to address these learning goals. In this study, the first group of student outcomes from this initiative are evaluated by the Test of Scientific Literacy Skills, Course-Based Undergraduate Research Experience Survey, and the Baylor Course Evaluation. Statistical analyses indicate significant gains in students’ skills in data analysis, accessing primary literature, identifying the validity of scientific arguments, collecting data, and learning laboratory techniques. While supporting the concept that inquiry-based courses improve students’ perception of science, thus providing an improved way to teach the process of science, these outcomes also indicate areas for improvement in qualitative skills.