Objective Eosinophilic esophagitis (EoE) is a chronic immune-mediated disease. The budesonide orodispersible tablet (BOT) is recommended as second-line treatment according to the Danish guideline. This study aimed to compare potential treatment disparities before BOT initiation, follow-up practices, clinico-histologic remission rates during BOT treatment, and adherence to the national guideline between the highly specialized EoE-Cph cohort and the population-based DanEoE cohort. Material and methods This cohort study compared 65 adult patients from the EoE-Cph cohort with 65 patients from the DanEoE cohort. All patients were diagnosed between 2015-2021. The diagnosis of EoE was defined according to the AGREE consensus. Data were extracted manually from medical records and registries. Results In the EoE-Cph cohort, 88% were prescribed proton pump inhibitors (PPIs) before started on BOT compared to 100% in the DanEoE cohort (p = 0.0035). Symptomatic follow-up occurred in 89% of EoE-Cph patients compared to 97% of DanEoE patients after BOT treatment (p = 0.0841). No difference was found between patients who underwent histologic follow-up after topical steroid treatment (83% versus 82%, p = 0.8162). Complete clinico-histologic remission was frequently observed, and no significant difference was observed between the two cohorts (67% versus 80%, p =0.1789). One out of four patients had conflicting symptomatic and histological responses. Conclusions This study did not provide conclusive evidence favoring the treatment of EoE patients exclusively at highly specialized EoE centers. However, the authors acknowledge that further evidence is necessary before considering changes in clinical practice. Conflicting treatment responses, and discontinuation of treatment due to side effects remains a notable concern.