Background: We assessed the effect of propolis on the antibacterial, mechanical, and adhesive properties of a commercial poly(alkenoate) cement. Methods: The cement was modified with various concentrations of propolis, and antibacterial assays were performed against S. mutans by both MTT assays and agar diffusion tests. The compressive, flexural, and adhesive properties were also evaluated. Results: the modified cement showed activity against S. mutans in both assays, although reductions in compressive (from 211.21 to 59.3 MPa) and flexural strength (from 11.1 to 6.2 MPa) were noted with the addition of propolis, while adhesive strength (shear bond strength and a novel pull-out method) showed a statistical difference (p < 0.05). Conclusion: the antiseptic potential of modified material against S. mutans will allow this material to be used in cases in which low mechanical resistance is required (in addition to its anti-inflammatory properties) when using atraumatic restorative techniques, especially in deep cavities.