Due to the ongoing COVID-19 pandemic, institutions across the world have had to make modifications to existing curricula throughout the university. Course-based Undergraduate Research Experiences (CUREs) are emerging as an effective way to offer research opportunities for students traditionally underrepresented in STEM. These types of courses face the unique task of adapting scientific conceptual and research process concepts to the distance learning format. Biochemistry Authentic Student Inquiry Lab (BASIL) is a freely available, modular CURE. This project showcases a two-pronged approach which combines student self-reported mastery and objective evaluation of lab report responses, both aligned with established Anticipated Learning Outcomes (ALOs) for BASIL. Using pre- and post-surveys, we measured growth in knowledge, experience, and confidence (KEC) as a result of taking the course. Students reported learning more about bioinformatic experiments and concepts better than their wet-lab counterparts. KEC tied directly to ALOs had an average gain score of 67.0% while those referring to techniques increased 61.5%. Student lab report responses aligned to ALOs were analyzed on a Likert scale from one to five. Due to the emergency shift online, this analysis has provided preliminary data on the mastery of biochemical ALOs during online learning. The students’ mastery of wet-lab ALOs coincided with our findings that lab courses need enhanced strategies to teach critical STEM lab-research skills in an online setting. Such novel assessment strategies developed based on learning objectives help fill this skills gap and enhance the exposure of undergraduate students to vital STEM research experiences.