Background: Despite an initial steep decrease in alcohol misuse among Estonians through structural intervention means and the scaling up of alcohol counselling in the mid-2000's, most of the country's alcohol misuse indicators remain clearly higher than European averages. Consequently, an online self-help program was launched as part of an initial behavioral intervention initiative to foster progress in alcohol prevention on a population level. Methods: A two-arm randomized controlled trial (RCT) has been designed to compare the efficacy of a culturally-adapted minimal-guidance online self-help program, the 8-week "Selge" online program against a control condition that consists of a self-administered test of alcohol use and advice regarding usual treatment in Estonia. A target sample of 600 individuals will be recruited and randomly assigned to either condition. The program will contain 10 modules based on principles of cognitive behavioural therapy (CBT) and motivational interviewing (MI). Participants in the control group will have access to the full treatment after they complete their final follow-up assessment. The primary outcome will be change in the Alcohol Use Disorders Identification Test (AUDIT) score between the 6-month follow-up and baseline assessments. Secondary outcomes will include the number of standard drinks consumed and alcohol-free days, drinking motives and motivation for change, as well as changes in mental health. Assessments will be completed at baseline, at the end of treatment, and at 6 months follow-up. Data analysis will follow the intention-to-treat principle and employ (generalised) linear mixed models. Discussion: The "Selge" program is the first and only internet program for the intervention of alcohol misuse in Estonia. If proven effective, it will foster progress in the intervention of alcohol misuse in the Estonian population and be implemented as a standard program amidst the continuum of intervention and care. Trial registration: Current Controlled Trials ISRCTN48753339 registered 04/06/2019 retrospectively.