Background and study aims Oropharyngeal intubation during Esophagogastroduodenoscopy (EGD) is uncomfortable, associated with aerosol generation and transmission of airborne microbes. Less-invasive alternatives may be better tolerated. In this study, patient tolerance and acceptability of EGD and transnasal endoscopy (TNE) have been compared with magnet-controlled capsule endoscopy (MACE). Patients and methods A comparison of MACE with EGD and TNE in the investigation of dyspepsia was performed. Factors affecting patient tolerance and acceptability were examined using the Endoscopy Concerns Scale (ECS) and Universal Patient Centeredness Questionnaire (UPC-Q). Results Patients were significantly more distressed (scoring least to most distress: 1–10) by gagging (6 vs 1), choking (5 vs 1), bloating (2 vs 1), instrumentation (4 vs 1), discomfort during (5 vs 1) and after (2 vs 1) EGD compared to MACE (all P < 0.0001). Patients were more distressed by instrumentation (5 vs 1) and discomfort during (5 vs 1) TNE compared to MACE ( P = 0.001). Patients were more accepting of MACE than EGD and TNE with a UPC-Q score (scoring least to most acceptable: 0–100) lower for EGD (50 vs 98, P < 0.0001) and TNE (75 vs 88, P = 0.007) than MACE, and a post-procedure ECS score (scoring most to least acceptable: 10–100) higher for EGD (34 vs 11, P < 0.0001) and TNE (25 vs 10.5, P = 0.001) than MACE. MACE would be preferred by 83 % and 64 % of patients even if EGD or TNE respectively was subsequently recommended to obtain biopsies in half of examinations. Conclusions Gagging and choking during instrumentation, the main causes of patient distress during EGD, occurred less during TNE but tolerance, acceptability and patient experience favored MACE.