Abstract Introduction Esophageal motility disorders present diagnostic and therapeutic challenges, with dysphagia being a common symptom prompting evaluation. The Endolumenal Functional Lumen Imaging Probe (EndoFLIP) has recently gained recognition as a valuable tool for assessing esophageal function. This study aims to evaluate the utility of EndoFLIP in guiding therapeutic interventions, specifically focusing on botulinum toxin injections, among patients presenting with diverse esophageal disorders. Moreover, the study acknowledges the potential of EndoFLIP as a diagnostic adjunct during diagnostic upper gastrointestinal endoscopy in cases where therapeutic alternatives are limited or as therapeutic trial. Methods A retrospective analysis was conducted on 21 patients who underwent EndoFLIP assessment and subsequently received botulinum toxin injection at the same procedure. These patients were identified from records at a tertiary center, covering the period from January 2022 to February 2023. EndoFLIP procedures were analyzed, focusing on patient symptoms and indication for the procedure. Data regarding clinical symptoms, EndoFLIP findings, and therapeutic interventions were extracted and analyzed to assess the role of EndoFLIP in guiding treatment decisions for esophageal disorders. The used cutoffs for esophagogastric junction (EGJ) distensibility index were < 2 mm2/mmHg and < 10 mm2/mmHg for pyloric distensibility. Results All patients referred for esophageal motility evaluation with EndoFLIP presented with dysphagia as the primary symptom. Two patients presented with postprandial bloating, leading to further evaluation with impedance planimetry to assess pyloric distensibility, suspected to be due to diabetic gastroparesis. Following EndoFLIP assessment, a conclusive diagnosis was achieved in all patients: 10 patients were diagnosed with esophagogastric junction outflow obstruction, 1 patient with absent contractility, 7 patients with achalasia, and 1 patient with hypercontractile esophagus. Patients who underwent planimetry to evaluate pyloric distensibility both exhibited reduced distensibility index. Following treatment, 10 patients showed clinical improvement and 11 await clinical reassessment. Conclusions Regarding the evaluation of the EGJ distensibility index in patients with achalasia without indication for invasive treatment, the EndoFLIP emerges as a diagnostic tool that allows for immediate guidance if intervention is recommended. Likewise, patients with refractory gastroparesis and pylorospasm identified through EndoFLIP may benefit from toxin injection for future myotomy decision. In conclusion, EndoFLIP serves as a valuable tool in diagnosing and guiding therapeutic interventions in patients with esophageal and gastric motility disorders. Further research is warranted to validate the role of EndoFLIP in optimizing treatment outcomes for esophageal disorders.