Background: Chronic otitis media with effusion (COME) and adenoid hypertrophy (AH) are common entities in the pediatric population. The conventional treatment approach (conventional medicine; COM) involved mainly surgery after a period of close observation. In this study, we aimed to introduce an integrative, non-invasive approach (integrative medicine; IM) for COME, AH, and associated episodes of recurrent acute otitis media, and compared outcomes with conventional treatment. Methods: We conducted a prospective, non-randomized study in an integrative primary care pediatric practice and a conventional pediatric otolaryngological clinic, where treatment modality was determined by patient preference. Out of a total 101 patients aged 1-8 years, integrative therapy was chosen by 46, and conventional treatment by 55. All patients had COME and AH diagnosed by an otolaryngologist and had moderate to severe hearing impairment. COM treatment was based on close observation over time, nasal decongestants and surgical intervention. In contrast, the IM involved a complex personalized approach with non-invasive interventions, non-allopathic medications, diet and patient education. Results: The number of surgical interventions (adenoidectomy, pressure-equalization tube insertion, myringotomy) was significantly less in the IM cohort (1 of 28 vs. 15 of 35 in the COM group, p < 0.001). The frequency of antibiotic use was significantly less in the IM group (p < 0.001). The frequency of analgesic use was also significantly less in the IM group (p = 0.029). Improvement in tympanometric measures (normal A-type curve) was higher in IM patients compared to expected spontaneous remission during the observation period. Improvement in audiometric measures (intact hearing) of IM patients was also higher than expected compared to spontaneous remission during the observation period. Conclusion: Compared to conventional treatment, integrative treatment of patients with COME and AH showed significantly lower invasive surgical intervention rates and significantly decreased antibiotic and analgesic use. The integrative treatment was effective, safe and well tolerated.