IntroductionApproximately 17% of adults with intellectual disabilities (ID) living in the community display behaviours that challenge. Intensive support teams (ISTs) have been recommended to provide high-quality responsive care aimed at avoiding unnecessary admissions and reducing lengthy inpatient stays in England. We have identified two models of ISTs (model 1: enhanced provision and model 2: independent provision). This study aims to investigate the clinical and cost-effectiveness of the two models of ISTs.Methods and analysisA cohort of 226 adults with ID displaying behaviour that challenges who receive support from ISTs from each model will be recruited and assessed at baseline and 9 months later to compare the clinical and cost-effectiveness between models. The primary outcome is reduction in challenging behaviour measured by the Aberrant Behaviour Checklist-Community (ABC-C). The mean difference in change in ABC score between the two IST models will be estimated from a multilevel linear regression model. Secondary outcomes include mental health status, clinical risk, quality of life, health-related quality of life, level of functioning and service use. We will undertake a cost-effectiveness analysis taking both a health and social care and wider societal perspective. Semistructured interviews will be conducted with multiple stakeholders (ie, service users, paid/family carers, IST managers/staff) to investigate the experience of IST care as well as an online survey of referrers to capture their contact with the teams.Ethics and disseminationThe study was approved by the London–Bromley Research Ethics Committee (REC reference: 18/LO/0890). Informed consent will be obtained from the person with ID, or a family/nominated consultee for those lacking capacity and from his/her caregivers. The findings of the study will be disseminated to academic audiences, professionals, experts by experience and arm’s-length bodies and policymakers via publications, seminars and digital platforms.Trial registration numberClinicalTrials.gov Registry (NCT03586375).