Background The diagnosis and management of bipolar disorder are limited by the absence of available biomarkers. Patients with bipolar disorder frequently present with mood instability even during remission, which is likely associated with the risk of relapse, impaired functioning, and suicidal behavior, indicating that the illness is active. Objective This research protocol aimed to investigate the correlations between clinically rated mood symptoms and mood/behavioral data automatically collected using the Toi Même app in patients with bipolar disorder presenting with different mood episodes. This study also aimed to assess the feasibility of this app for self-monitoring subjective and objective mood/behavior parameters in those patients. Methods This open-label, nonrandomized trial will enroll 93 (31 depressive, 31 euthymic, and 31 hypomanic) adults diagnosed with bipolar disorder type I/II (Diagnostic and Statistical Manual of Mental Disorders, 5th edition criteria) and owning an iPhone. Clinical evaluations will be performed by psychiatrists at the baseline and after 2 weeks, 1 month, 2 months, and 3 months during the follow-up. Rather than only accessing the daily mood symptoms, the Toi Même app also integrates ecological momentary assessments through 2 gamified tests to assess cognition speed (QUiCKBRAIN) and affective responses (PLAYiMOTIONS) in real-life contexts, continuously measures daily motor activities (eg, number of steps, distance) using the smartphone’s motion sensors, and performs a comprehensive weekly assessment. Results Recruitment began in April 2018 and the completion of the study is estimated to be in December 2021. As of April 2019, 25 participants were enrolled in the study. The first results are expected to be submitted for publication in 2020. This project has been funded by the Perception and Memory Unit of the Pasteur Institute (Paris) and it has received the final ethical/research approvals in April 2018 (ID-RCB: 2017-A02450-53). Conclusions Our results will add to the evidence of exploring other alternatives toward a more integrated approach in the management of bipolar disorder, including digital phenotyping, to develop an ethical and clinically meaningful framework for investigating, diagnosing, and treating individuals at risk of developing bipolar disorder or currently experiencing bipolar disorder. Further prospective studies on the validity of automatically generated smartphone data are needed for better understanding the longitudinal pattern of mood instability in bipolar disorder as well as to establish the reliability, efficacy, and cost-effectiveness of such an app intervention for patients with bipolar disorder. Trial Registration ClinicalTrials.gov NCT03508427; https://clinicaltrials.gov/ct2/show/NCT03508427 International Registered Report Identifier (IRRID) DERR1-10.2196/18818