The objective of this study was to assess how the application mode of a universal adhesive system affects the microshear bond strength (μSBS) of bulk-fill and conventional composite resins to enamel and dentin in primary teeth. A total of 80 caries-free primary second molars were randomly assigned to eight experimental groups (n = 10) based on the bonding substrate (enamel or dentin), the application mode of the universal adhesive system (etch and rinse [E&R], or self-etch [SE]), and the type of composite resin used (bulk-fill or conventional). After bonding the composite resin to enamel or dentin, the μSBS of the bonded composite resins was measured. The mean μSBS value of bulk-fill composite resin was significantly higher than that of conventional composite resin for both enamel and dentin substrates, regardless of the application mode (p < 0.001). An interaction effect between the bonding substrate and the application mode of the adhesive system was observed, indicating a significant relationship (p < 0.001). The highest μSBS values for primary teeth enamel were achieved using the E&R mode with bulk-fill composite resin, while for dentin specimens, the SE mode with bulk-fill composite resin yielded the highest μSBS values. The μSBS of the E&R group was significantly higher than that of the SE group for enamel specimens (p < 0.001), whereas the μSBS of the SE group was significantly higher than that of the E&R group for dentin specimens (p < 0.001). Bulk-fill composite resin demonstrated higher μSBS in comparison to conventional composite resin. The universal adhesive system exhibited superior performance in the SE mode compared to the E&R mode on primary dentin. Pre-etching the enamel before the application of the universal adhesive enhanced the μSBS to primary teeth enamel, highlighting the importance of selectively acid etching the enamel of primary teeth.