Implant abutment selection is an important step in implant treatment to restore one or more lost teeth. The aim of this study was to compare stock and individual CAD/CAM full-form abutments after one year in function. A total of 64 subjects with one missing tooth were divided into two groups according to the type of abutment: 34 patients were given a stock abutment, and 30 an individual CAD/CAM abutment. Patients were scheduled for check-ups seven days after functional loading and after four, eight, and twelve months. Peri-implant soft tissue status was checked at every check-up by monitoring parameters traditionally used in similar studies: plaque index; bleeding on probing; and probing depth. To assess the stability of the bone tissue, radiological methods of measuring the amount of bone level compared to the implant shoulder were used. When needed, data were analysed by χ2 test or by Fisher’s exact test. The normality of the distribution of quantitative measurements (properties) was tested by the Shapiro–Wilk test. Differences in the distribution of quantitative variables frequencies were analysed by Student’s t-test. Student’s t-test was used for repeated measurements, Mann–Whitney’s U test and ANOVA test for repeated measurements, and Friedmann’s two-way analysis of variance for repeated measurements. The predictive values of the chosen variables on the ABI index were assessed by the logistic regression model (Enter method). The results of this study showed that the impact of the abutment type (individual CAD/CAM or stock) on the average bleeding on probing was significant, especially after eight or twelve months. However, the abutment type did not show a significant correlation with the total crestal bone loss. The level of oral hygiene showed a significant correlation with the average bleeding on probing. The influence of smoking cigarettes on the total crestal bone loss evaluation was also significant. Overall, from a clinical perspective, custom CAD/CAM abutment performed slightly better than stock abutments during the one-year follow-up.