This study assessed the effect of different smear layers and surface conditioning on microtensile bond strength to dentin of two different glass-ionomer cements (GICs). Third molar teeth without caries were collected for this study. The crowns of teeth were cut to reveal the mid-coronal dentin surface, and then the specimens were randomly assigned to three groups for surface preparation (#180-grit, 600-grit, and #3000-grit SiC paper). After surface grinding, the specimens were restored by Equia Forte or Fuji II LC (GC, Tokyo, Japan). A buildup of each material was made by free-hand on the dentin surfaces with or without a polyacrylic acid conditioner. GIC/dentin sticks were obtained after 1 week storage and then stressed using a universal testing device. The fractured surfaces were examined by a stereomicroscope. Statistical analyses were performed with three-way ANOVA and Tukey's post-hoc test (p < 0.05). GIC type and conditioner application had a significant effect on mu TBS (p < 0.001). The smear layer conditions did not affect mu TBS of the GICs (p = 0.113). Only Equia Forte without conditioner showed significantly higher mu TBS on the #3000-grit surface than on #180-grit and #600-grit surfaces. Equia Forte presented significantly lower mu TBS than Fuji II LC, with or without conditioner. With conditioner application, both GICs showed significantly higher mu TBS on the #180-grit surface. The effect of different smear layers on mu TBS was dependent on GIC type and conditioner application. The effectiveness of the conditioner application to the bond strength depended on the smear layer composition.