Recent advances in biological therapies have revolutionalised and redefined treatment targets in inflammatory bowel disease (IBD). There is now a stronger emphasis on achieving the more stringent therapeutic goals of mucosal and histological healing, rather than clinical remission alone. Consequently, the treatment of refractory "functional" gastrointestinal symptoms, often attributed as the aftermath of previous inflammation, has recently become more prominent in quiescent disease. With further expected advances in anti-inflammatory treatments on the horizon, the burden of such symptoms in quiescent disease, which have been relatively neglected, is set to become an even bigger problem. In this article, we highlight the current state of research and understanding in this field, including recent developments and clinical practice guidelines on the diagnosis and management of functional gastrointestinal symptoms, such as irritable bowel syndrome and functional anorectal and pelvic floor disorders, in patients with quiescent IBD. These disorders are not only highly prevalent in these patients, they are often misdiagnosed, and are difficult to treat, with very few evidence-based therapies. Moreover, they are associated with substantial impairment in quality-of-life, considerable morbidity, and psychological distress. There is therefore an urgent need for a change in emphasis towards earlier recognition, positive diagnosis, and targeted treatment for patients with ongoing functional gastrointestinal symptoms in the absence of active IBD. This article also highlights the need for further research to develop much needed evidence-based therapies.