The assessment of microgaps at the implant–abutment interface is an important factor that may influence clinical success. Thus, the aim of this study was to evaluate the size of microgaps between prefabricated and customised abutments (Astra Tech, Dentsply, York, PA, USA; Apollo Implants Components, Pabianice, Poland) mounted on a standard implant. The measurement of the microgap was performed using micro-computed tomography (MCT). Due to 15-degree rotation of samples, 24 microsections were obtained. Scans were performed at four levels established at the interface between the abutment and the implant neck. Moreover, the volume of the microgap was evaluated. The size of the microgap at all measured levels varied from 0.1 to 3.7 µm for Astra and from 0.1 to 4.9 µm for Apollo (p> 0.05). Moreover, 90% of the Astra specimens and 70% of the Apollo specimens did not exhibit any microgaps. The highest mean values of microgap size for both groups were detected at the lowest portion of the abutment (p> 0.05). Additionally, the average microgap volume was greater for Apollo than for Astra (p> 0.05). It can be concluded that most samples did not exhibit any microgaps. Furthermore, the linear and volumetric dimensions of microgaps observed at the interface between Apollo or Astra abutments and Astra implants were comparable. Additionally, all tested components presented microgaps (if any) that were clinically acceptable. However, the microgap size of the Apollo abutment was higher and more variable than that of the Astra one.