Purpose Cold atmospheric plasma can functionalize enamel without damaging the substrate morphology. It therefore has the potential to be a gentle alternative to conventional acid etching. To realize the full potential of cold atmospheric plasma in orthodontic bonding, the input parameters and protocols that are most beneficial to surface modification must first be identified. We aimed to clarify how the admixture of oxygen to cold atmospheric plasma and the rewetting of the enamel affect the conditioning properties for orthodontic bonding. Methods First, we illustrated the morphological effects of different plasma compositions on the enamel surface by means of scanning electron microscopy. Then, we measured the shear bond strength resulting from different conditioning techniques on bovine enamel specimens: conventional acid etching; no conditioning; pure argon plasma; argon plasma plus 0.5% oxygen admixture; argon plasma plus 0.5% oxygen and rewetting after plasma application. Brackets were bonded using light cured adhesive; all specimens were subjected to thermocycling. The shear bond strength of each specimen was measured in a universal testing machine and compared using Welch one-way analysis of variance (ANOVA) and Games–Howell post hoc test. Results Specimens conditioned with argon plasma plus 0.5% oxygen and rewetting showed a significantly higher shear bond strength than specimens conditioned with conventional acid etching. Conditioning with pure argon plasma and argon plasma plus 0.5% oxygen without rewetting yielded significantly lower shear bond strength. Conclusion Admixing 0.5% oxygen and rewetting the enamel after plasma application are crucial steps that could help make cold atmospheric plasma a gentle conditioning technique in orthodontic bonding.