We developed and validated a new classroom observation protocol, Online COPUS (E-COPUS), to measure teaching and learning practices in the online learning environment. We collected COPUS and E-COPUS data from 40 STEM courses before, during the transition, and continuation of emergency remote teaching (ERT). Through weekly discussions among observers, we adjusted six of the original instructor COPUS code descriptions and six of the original student code descriptions to fit the online learning environment. We trained 23 observers to conduct E-COPUS utilizing both in-person and online lecture recordings. To validate E-COPUS, we consulted an expert panel of science educators and education researchers to provide feedback on our code descriptions and complete a matching activity with our E-COPUS code descriptions. We further examined E-COPUS by analyzing the teaching and learning practices of 6 instructors across in-person and online instruction and found that the online functions of breakout rooms, polling, and the chat were utilized to promote active learning activities in the online learning environment. As we prepare for teaching in the future, it is important to have formative assessment tools designed for all course formats to support assessment and improvement of teaching practices in college STEM classrooms.