This paper examines the pedagogical integration of Virtual Microscopes (VMs) in Virtual Learning Environments (VLEs), to identify best practice and improve online pedagogy. It has captured the perspectives of 12 Health and Earth Science university teachers, through in-depth interviews, about the current integration of the VM in online teaching, benefits and challenges, and their recommendations for enhancing online and distance learning. Findings revealed that the VM has been integrated in online courses in varied ways, addressing diverse learning objectives. Teachers noted two particular challenges: (a) the need for support throughout the lifecycle of a course, and while students are using the VM, that will complement the introductory support currently provided, and (b) the design of VM learning activities that promote higher order thinking skills. Implications about the significance of engaging teachers with the process of designing online courses and using the VM to enable remote learning in cases of emergency are discussed.