This study aims to develop and evaluate an augmented reality microscope, "MicrosAR", for a middle school Science course, which was aimed for use both in and out of school, and to understand the users' perceptions about it. The study adopted design-based research to iteratively develop and evaluate the MicrosAR. Learning activities and working handouts in the application were grounded upon inquiry-based learning. The initial prototype was evaluated with 99 middle school students, as well as 18 preservice and six experienced in-service science teachers. The second prototype was then evaluated with 96 different middle school students. Accordingly, design changes were applied to the second prototype to present the final product development. Participants' experiences and perceptions were gathered through a self-developed, paper-based instrument after they practiced with the MicrosAR. The findings indicated that the MicrosAR was favored by and recognized as an effective and useful tool by the participants. The study highlighted the benefits that augmented reality technology and such an application can offer for learning purposes, and that it can be practiced at any place to deliver a "real" learning experience over virtual platforms, thereby saving costs, enhancing its availability, and improved learner interest.