Background: Recurrent wheezing and gastroesophageal reflux disease (GERD) are common in young children, with a suggested but challenging link between them. This study aimed to investigate the diagnostic value of pH-MII monitoring in preschool children with recurrent wheezing and evaluate GERD-related therapy effects. Methods: Children under 6 years with recurrent wheeze were eligible. The pH-MII monitoring was conducted in those clinically suspected of GERD’s involvement. Flexible bronchoscopy with bronchoalveolar lavage (BAL) was performed in severe cases. The primary outcome was the difference in wheezing episodes between proven GERD and non-GERD groups. Secondary outcomes included GERD therapy impact and predictive factors for wheezing reduction. Results: Of 66 children (mean age 3.9 years), 71% had proven GERD on pH-MII. Compared to the non-GERD group, the GERD group had higher total, liquid, mixed, and gas reflux episodes, as well as more acidic and weakly acidic episodes. GERD treatment significantly reduced wheezing episodes. PPI (proton pump inhibitor) introduction was associated with ≥50% wheezing reduction. Children with GERD showed ≥50% wheezing reduction more frequently than those without GERD. PPI usage, higher total GER episodes, acidic episodes, and liquid and proximal episodes on MII predicted ≥50% wheezing reduction. No significant BAL differences were observed between GERD and non-GERD groups. Conclusions: The pH-MII monitoring is valuable in diagnosing GERD-related wheezing in preschool children. GERD therapy, particularly PPI usage, was associated with reduced wheezing episodes. The pH-MII parameters correlated with wheezing reduction, suggesting their potential predictive role. BAL did not differentiate between GERD and non-GERD cases.