The aim of this study was to evaluate the effect of different surface treatments on the microtensile bond strength (μTBS) of two different self-adhesive flowable composite materials (SACs) to dentin. Forty extracted human molars were horizontally flattened to expose the dentin surfaces. The teeth were divided into eight groups according to the surface treatments (acid etching, Er:YAG laser quantum square pulse (QSP) mode, and Er:YAG laser medium-short pulse (MSP) mode at 10 Hz, 1.2 W, 120 mJ, and control-SiC) and SAC type (Vertise Flow and Fusio Liquid Dentin) (n = 5). Light cured 4-mm-high composite build-ups were made on the dentin surfaces, and the specimens were sectioned into serial sticks (n = 15). Later, the specimens were attached to microtensile testing machine and tensile force was applied at a crosshead speed of 1 mm/min until failure occurred. The failure modes were evaluated using a stereomicroscope at ×40 magnification, and one sample from each group was used for scanning electron microscopy (SEM) evaluation. The data were analyzed with two-way ANOVA and Tukey’s HSD test (α = 0.05). In all surface treatment groups along with the control groups, Vertise Flow showed better μTBS than the Fusio Liquid Dentin with the exception of the Er:YAG MSP mode surface treatment (p < 0.05). Etching with phosphoric acid and the Er:YAG QSP mode surface treatment significantly increased the μTBS of Vertise Flow (p < 0.05). Etching with phosphoric acid, Er:YAG QSP mode surface treatment, and Er:YAG MSP mode surface treatment significantly increased the μTBS of Fusio Liquid Dentin (p < 0.05). The μTBS of Vertise Flow was higher than the μTBS of Fusio Liquid Dentin. The Er:YAG laser irradiation increased the μTBS of both self-adhesive flowable resin composites in two pulse modes tested (MSP or QSP). However, the highest μTBS was recorded when Vertise Flow was applied with acid etching.