Enzymes in toothpastes can support host immune responses, and thus maintain oral health. This study aimed to investigate gingival health and the plaque-reducing effects of enzyme-containing toothpastes. A laboratory study tested the antimicrobial potential of different enzyme-containing toothpaste formulations. Two promising formulations (enzyme-containing toothpastes with glucose oxidase and D-glucose with (C+) and without Citrox (C−) Citrox) were investigated in a clinical crossover trial (two slurries: sodium lauryl sulfate-containing (SLS), a toothpaste without SLS (reference), and water). Subjects (n = 20) abstained from toothbrushing for four days and rinsed with a toothpaste slurry. Bleeding on probing (BOP) and plaque indices (PI) were measured. A mixed linear model was used to statistically compare the slurries with respect to BOP and PI change. The in vitro bacterial growth-inhibiting evaluation showed the best results for SLS, followed by C+ and C−. The change in BOP and PI exhibited statistically significant differences to water rinsing (BOP; PI changes in % points (difference of the baseline and post-rinse values: water = 8.8%; 90.0%; C+ = −1.4%; 80.4%; SLS = 1.5%; 72.1%; reference = 0.8%; 77.5%; C− = −1.8%; 75.1%). All slurries exhibited anti-gingivitis and anti-plaque effects, resulting in a prophylactic benefit for limited-access regions during brushing.