Abstract Background Upper GI surgery, and particularly upper GI cancer surgery can result in quality of life limiting symptoms months and years later. While some of these symptoms may be unavoidable, there are a number of conditions which can be treated with the intention of improving quality of life. We developed and assessed the impact of a CNS and dietitian-led protocol for the investigation and management of late effects after upper GI cancer surgery at Addenbrooke’s Hospital, Cambridge. Methods A multi-disciplinary team including nurses, dietitians, pharmacists and with medical input from surgery, gastroenterology and clinical biochemistry produced a pragmatic guideline for the investigation and management of gastrointestinal, nutritional and endocrinological late effects. The protocol was instituted then retrospectively assessed for impact. The patients were divided in two groups, according to the beginning of their investigations: before or after the introduction of the protocol. Key measures were: proportion of patients being investigated for late effects, the time from presentation of symptoms to diagnosis and which late effects patients were diagnosed. Results In the analysis we included a total of 63 patients, 43 from the pre-protocol group and 20 from the post-protocol group. Patients investigated more than once have been interpreted individually making 51 cases pre-protocol and 22 post-protocol. In the pre-protocol group, 78.43% of patients were investigated for late effects. Among them 55% were diagnosed SIBO, 22.9% PEI. In the post-protocol group, 36.36% of patients were investigated for late effects. Among them 50% were diagnosed SIBO and 37.5% PEI. The average time from symptoms to diagnosis in the pre-protocol group was 10 months while in the post-protocol group 2 months. Conclusions The protocol has proved a popular adjunct to AHP-led follow-up clinics. The time from symptom onset to diagnosis has significantly improved from 10 to 2 months with the new protocol. Interestingly, the protocol appears to have reduced the number of patients investigated, however as the proportion of patients with SIBO has not changed, suggesting some patients may not be being identified. However, this may reflect the small study numbers and will likely change over time. We are keen to demonstrate our early experience with this standardised, nurse/dietitian-led approach to management of symptoms after Upper GI cancer surgery.