Abstract Background The factors that influence transition from suicidal ideation to a suicide attempt or remission of suicidal thoughts are poorly understood. Despite an abundance of research on risk factors for suicidal ideation, no large-scale longitudinal population-based studies have specifically recruited people with suicidal ideation to examine the mechanisms underlying critical transitions to either suicide attempt or recovery from suicidal ideation. Without longitudinal data on the psychological, behavioural, and social determinants of suicide attempt and the remission of suicidal ideation, we are unlikely to see major gains in the prevention of suicide. Aim The LifeTrack Project is a population-based longitudinal cohort study that aims to identify key modifiable risk and protective factors that predict the transition from suicidal ideation to suicide attempt or remission of suicidal ideation. We will assess theory-informed risk and protective factors using validated and efficient measures to identify distinct trajectories reflecting changes in severity of suicidal ideation and transition to suicide attempt over three years. Methods A three-year prospective population-based longitudinal cohort study will be conducted with adults from the general Australian population who initially report suicidal ideation (n = 842). Eligibility criteria include recent suicidal ideation (past 30 days), aged 18 years or older, living in Australia and fluent in English. Those with a suicide attempt in past 30 days or who are unable to participate in a long-term study will be excluded. Participants will be asked to complete online assessments related to psychopathology, cognition, psychological factors, social factors, mental health treatment use, and environmental exposures at baseline and every six months during this three-year period. One week of daily measurement bursts (ecological momentary assessments) at yearly intervals will also capture short-term fluctuations in suicidal ideation, perceived burdensomeness, thwarted belongingness, capability for suicide, and distress. Conclusion This study is intended to identify potential targets for novel and tailored therapies for people experiencing suicidal ideation and improve targeting of suicide prevention programs. Even modest improvements in current treatments may lead to important reductions in suicide attempts and deaths. Study Registration Australian New Zealand Clinical Trials Registry identifier: ACTRN12623000433606.