The COVID-19 shutdown forced many institutions of higher education to shift in-person teaching to emergency remote teaching. This was particularly challenging for laboratory courses, where students are expected to learn hands-on skills needed for their career goals. Here, we describe the transformation of an upper-division microbiology laboratory to a course that seamlessly integrates online simulations with safe, hands-on experiences that can be done from home. This blended lab course helped students attain learning outcomes similar to those achieved in the in-person class. We illustrate the implementation of Unknown Portfolios to help students gain the data analysis and critical thinking skills needed to identify an unknown microorganism. Our data show that students who took these online courses mastered material as well as students who took the lab in person, demonstrating proficiency in laboratory safety skills, hands-on techniques, and theoretical class content. Last, we explore online adaptations to enhance in-person lab classes, aiming at reducing the accessibility and equity gaps inherited in many courses, as well as discussing challenges that instructors might experience in this process.