The coronavirus (COVID-19) outbreak mandated a rapid transition to online classes with little warning. Previous literature studying the effect of this sudden shift demonstrated enormous impacts on instructors and students. However, the details concerning science instructor assessment choices during this time are less clear. We asked biology instructors to reflect on the changes they made to their assessments of student learning during the emergency transition to remote instruction in spring of 2020 and whether the potential changes were motivated by equity concerns. We also asked that instructors describe the assessment changes they intended to keep in future semesters. Through quantitative and qualitative analyses, we found that instructors removed forms of assessment more often than they added them, and the most common changes included how instructors administered exams and engaged students through participation. Instructors reported that equity concerns motivated their decision-making, particularly their concern over students’ ability to access learning resources. Instructors indicated they would keep many of the changes they made in response to COVID-19. Our research shows the pandemic dramatically altered how instructors assessed students in biology, but equity-based decisions leading to lasting change may be one positive outcome for future students.