We have investigated the effect of non-thermal atmospheric pressure plasma (NTAPP) treatment and the post process time on the bonding strength and surface sterilization of dental zirconia. Presintered zirconia specimens were manufactured as discs, and then subjected to a 30-min argon treatment (Ar, 99.999%; 10 L/min) using an NTAPP device. Five post-treatment durations were evaluated: control (no treatment), P0 (immediate), P1 (24 h), P2 (48 h), and P3 (72 h). The surface characteristics, shear bonding strength (SBS) with two resin cements, and Streptococcus mutans biofilm formation of these plasma-treated dental zirconia were tested. Plasma did not change the roughness, and caused surface element changes and surface energy increase. Due to this increase in surface energy, SBS increased significantly (p < 0.05) within 48 h when RelyXTM U200 was used. However, the increase of surface oxygen significantly decreased (p < 0.05) the SBS of Panavia F 2.0 when using plasma immediately (P0). S. mutans adhesion decreased significantly (p < 0.05) for the P0, P1, and P2 groups compared to the control. The P0 group exhibited lower biofilm thickness than the other experimental groups due to the increased hydrophilicity (p < 0.05). Our study suggests that there is a suitable time window for the post NTAPP treatment regarding bonding strength and antimicrobial growth persist.