The objective of this work was to assess the efficacy of different proteolytic agents on the bond strength of pit and fissure sealants to bovine enamel. Eighty-four bovine enamel specimens were randomly assigned in groups according to the pit and fissure sealant applied (HelioSeal F or Dyad Flow). Then, the specimens were subdivided according to the proteolytic agent used (n = 7): Group 1, distilled water (control); Group 2, 10 wt.% Tergazyme®; Group 3, 10 wt.% ZYME®; Group 4, 10% papain gel; Group 5, 10% bromelain gel; and Group 6, 5.25 wt.% sodium hypochlorite. The cell viability of the proteolytic solutions was assessed through the MTT assay. The proteolytic agents were applied on the enamel surface prior to the acid-etching procedure; then, the pit and fissure sealants were placed. The micro-shear bond strength was evaluated after 24 h or 6 months of water storing at 37 °C. Representative SEM images were taken for each experimental group. The bond strength data were statistically analyzed by a three-way ANOVA test using a significance level of α = 0.05. Bromelain and papain proteolytic solutions did not exert any cytotoxic effect on the human dental pulp cells. After 24 h and 6 months of aging, for both pit and fissure sealants, sodium hypochlorite, papain, bromelain, and Tergazyme® achieved statistically significant higher bond strength values (p < 0.05). Irrespective of the deproteinizing agent used, Dyad Flow resulted in a better bond strength after 6 months of aging. The type 1 etching pattern was identified for sodium hypochlorite, papain, and bromelain. Tergazyme®, papain, and bromelain demonstrated efficacy in deproteinizing enamel surfaces prior to acid etching, leading to the improved bond strength of pit and fissure sealants. Clinically, this suggests that these proteolytic agents can be considered viable alternatives to traditional methods for enhancing sealant retention and longevity. Utilizing these agents in dental practice could potentially reduce sealant failures.