Introduction Older adults (65 years or over) and those with long-term health conditions (LTCs), represent a ‘high risk’ group for depression, with a risk two-to-three times the general population. This can lead to poorer quality of life and be costly to health and social care services. In the Multimorbidity in Older Adults with Depression Study (MODS) we will test whether a brief psychological intervention (Behavioural Activation), helps to improve physical/mental functioning in this group compared to treatment as usual. Methods We will conduct a two-arm, parallel-group randomised controlled trial, to evaluate the clinical and cost-effectiveness of the MODS intervention. Participants will be recruited via general practices across England. To be included, participants must be aged 65 years or over, with two or more LTCs and either sub-threshold depression or major depression. Randomisation will be simple 1:1. Intervention participants will receive up to eight sessions delivered by MODS support workers, supported by a self-help booklet. Control participants will receive usual care. A process evaluation will be undertaken to evaluate the processes and mechanisms underpinning intervention delivery, and to inform the development of an implementation framework. Semi-structured interviews will be conducted with intervention participants, participant’s caregivers/supportive others, and health and social care professionals. Focus groups and semi-structured interviews will be conducted with MODS support workers. Outcome data will be collected at four, eight, and twelve-months post-randomisation. The primary outcome is self-reported quality of life and functioning at the four-month follow up. Secondary outcomes include depression, anxiety, physical functioning, loneliness, social isolation, chronic pain, health related quality of life, and health services use. Discussion This study builds on our previous work and will evaluate a brief psychological intervention to improve physical and mental health functioning for older adults with multiple long-term conditions. Trial Registration ClinicalTrials.Gov IdentifierISRCTN44184899, registered on 11th August 2022.