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The aim of this study was to report on the clinical experience with microscope-based augmented reality (AR) in transsphenoidal surgery compared to the classical microscope-based approach. AR support was established using the head-up displays of the operating microscope, with navigation based on fiducial-/surface- or automatic intraoperative computed tomography (iCT)-based registration. In a consecutive single surgeon series of 165 transsphenoidal procedures, 81 patients underwent surgery without AR support and 84 patients underwent surgery with AR support. AR was integrated straightforwardly within the workflow. ICT-based registration increased AR accuracy significantly (target registration error, TRE, 0.76 ± 0.33 mm) compared to the landmark-based approach (TRE 1.85 ± 1.02 mm). The application of low-dose iCT protocols led to a significant reduction in applied effective dosage being comparable to a single chest radiograph. No major vascular or neurological complications occurred. No difference in surgical time was seen, time to set-up patient registration prolonged intraoperative preparation time on average by twelve minutes (32.33 ± 13.35 vs. 44.13 ± 13.67 min), but seems justifiable by the fact that AR greatly and reliably facilitated surgical orientation and increased surgeon comfort and patient safety, not only in patients who had previous transsphenoidal surgery but also in cases with anatomical variants. Automatic intraoperative imaging-based registration is recommended.