There is an increasing appreciation of the role that the host microbiome plays in the progression of oesophageal diseases. To date, potential relationships between the microbiota and the development of gastro-oesophageal reflux disease, Barrett’s oesophagus, oesophageal adenocarcinoma, oesophageal squamous cell carcinoma, eosinophilic oesophagitis, and achalasia have been reported. Studies have not been limited to the local oesophageal microbiota but have also examined the oral and lower gut microbiotas. Comprehensive literature searches were performed on these topics for articles published from April, 2019 to March 2020 to provide an update on associations between the microbiota and oesophageal disease. The identified studies generally comprised cross-sectional profiling of differences in the microbiome between cases and controls. One robust study examined a mouse model of Barrett’s oesophagus expressing human interleukin (IL)-1B and found that high fat diet accelerated the development of dysplasia partly through modifying the gut microbiota and this was independent of obesity. A substantial number of studies associated viral infections with oesophagitis; however, surprisingly, to date no virome studies have been attempted. Research areas currently lacking include holistic analyses of different microbiotas in the context of oesophageal disease, metabolomic studies, as well as studies profiling the virome and mycobiome. The oral, oesophageal and gut microbiota appear to play some role in the development of oesophageal disease; however, causation is currently absent in most published studies.