Background: Adapalene–benzoyl peroxide (A-BPO) is a first-line topical treatment for acne vulgaris. In vivo reflectance confocal microscopy (RCM) and optical coherence tomography (OCT) detect micromorphological changes over time and visualize transfollicular delivery. Objectives: To visualize temporal, subclinical effects of A-BPO on acne micromorphology using RCM and OCT, and evaluate their impact on transfollicular delivery of microparticulate carrier systems. Methods: Fifteen patients with mild to moderate acne received a 6-week course of A-BPO. Micromorphological changes were evaluated at time 0, 3 and 6 weeks with RCM (n = 1190 images) and OCT (n = 210 scans). Transfollicular delivery of microparticles was assessed at baseline and week 6. Results: In vivo imaging visualized steady normalization of skin micromorphology in response to A-BPO over 6 weeks, including decreased hyperkeratinization of follicular borders (RCM median decrease −71.2%, P < 0.05), reduced intrafollicular keratinous content (RCM median decrease −47.7%, P < 0.05) and increased epidermal thickness (OCT median increase of 25.25%, P < 0.05). Imaging visualized microparticles in the follicular unit. Despite a visible reduction in keratin and sebum, transfollicular microparticle delivery appeared unaffected. Conclusions: Reflectance confocal microscopy and OCT detect A-BPO-induced changes in micromorphology and visualize transfollicular microparticle delivery. Keratolysis and sebolysis did not have a measurable effect on transfollicular delivery of microparticles.