Background: While phosphoric acid etching is standard for resin-based sealants, its effect on glass ionomer and giomer sealants remains less explored. This in vitro study evaluated the shear bond strength (SBS) of various fissure sealant materials applied to bovine enamel using different surface conditioning methods (phosphoric acid, conditioner, or no pretreatment). Methods: 100 bovine incisors were prepared and divided into four material groups: Fuji TRIAGE® (FT; n = 30), Riva Protect® (RP; n = 30), BeautiSealant® (BT; n = 30), and Helioseal F Plus® (HF; control, n = 10). Specimens were assigned to subgroups based on pretreatment: 37% phosphoric acid, material-specific conditioner, or no pretreatment. SBS testing was performed according to the International Organization for Standardization (ISO) 29022 standards. Bonding failure types were classified according to the Adhesive Remnant Index under 25× magnification using a ZEISS OPMI® pico S100 microscope. Data were analyzed using one-way analysis of variance (ANOVA), chi-squared, and Bonferroni tests (p < 0.05). Results: Significant differences were observed (p < 0.001). The control group (HF) demonstrated the highest SBS (15.21 ± 1.15 MPa). Among the alternative materials, BT pretreated with phosphoric acid (13.18 ± 2.96 MPa) showed significantly higher SBS than with a self-etching primer (10.23 ± 1.85 MPa). Furthermore, the BT exhibited significantly higher bond strength values than both glass ionomer-based sealants (FT and RP) across all conditioning protocols. Adhesive failures were predominant in groups with lower bond strengths. Conclusions: Resin-based fissure sealant applied with phosphoric acid etching demonstrated the highest SBS values among all tested groups. However, the giomer-based sealant exhibited superior bonding performance compared with the glass ionomer-based sealants. Additionally, phosphoric acid etching significantly enhanced the adhesion of the giomer material, suggesting that surface conditioning plays a crucial role in maximizing the retention of bioactive sealants.