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Traditional surface area and volume quantification techniques for scleractinian corals are often destructive or inaccurate. Therefore, non-destructive 3D scanning methods have been applied as minimally invasive alternative. However, it remains largely unknown how the reproducibility of the measurement is affected by the complexity of the coral colonies. It is also unclear how the scanning procedure (handling, exposure to air, and light of the scanner) impacts the corals’ health. In this study, we used a high-end handheld 3D scanner, which combines a structured-light with an image-based approach, to investigate the reproducibility of surface area and volume measurements as well as handling effects. Corals with different shape complexity, covering branching and massive species, were used as model organisms. The variance of repetitive scans ranged from 0.13% to 1.31% for volume and from 0.09% to 0.58% for surface area calculations. Linear regression models indicated that reproducibility decreases with increasing complexity of the coral. Excessive scanning caused an increase or decrease of growth rates, depending on the studied species. However, it did not impair coral health. We conclude that 3D scanning is a highly precise, reproducible, and minimally invasive method for coral surface area and volume measurements, which allows for quick processing of large datasets. Detailed technical recommendations for the application of 3D scanning in coral research are provided in the manuscript.