Abstract Background Mental disorders are common during the peripartum period and may have far-reaching consequences for both mother and child. Unfortunately, most antenatal care systems do not provide any structured screening for maternal mental health. As a consequence, mental illnesses are often overlooked and not treated adequately. If correctly diagnosed, cognitive behavioral therapy is currently the treatment of choice for mental illnesses. In addition, mindfulness-based interventions (MBIs) seem to represent a promising treatment option for anxiety and depression during the peripartum period. Considering the internet’s increasing omnipresence, MBIs can also be offered electronically via a (tablet) computer or smartphone (electronically based MBI = eMBI). Objective The current study aims to examine the clinical effectiveness and cost-effectiveness of an eMBI (the mindmom application) developed by an interdisciplinary team of gynecologists, psychologists, and midwives, teaching pregnant women how to deal with stress, pregnancy-related anxiety, and depressive symptoms. The study sample consists of pregnant women in their third trimester who screened positive for emotional distress. The mindmom study is a bicentric prospective randomized controlled trial (RCT), which is currently conducted at the University women’s hospitals of Heidelberg and Tübingen, Germany. Methods Within the scope of the routine prenatal care, pregnant women attending routine pregnancy care in Baden-Wuerttemberg, Germany, are invited to participate in a screening for mental distress based on the Edinburgh Postnatal Depression Scale (EPDS). Women with an EPDS screening result > 9 will be referred to one of the mindmom coordinating study centers and are offered counseling either face-to-face or via videotelephony. After an initial psychological counseling, women are invited to participate in an eMBI in their last pregnancy trimester. The study will enroll N = 280 study participants (N = 140 per group), who are randomized 1:1 into the intervention (IG) or control group (treatment as usual = TAU). All participants are requested to complete a total of 7 digital assessments (5 visits pre- and 2 follow-up visits postpartum), involving self-report questionnaires, sociodemographic and medical data, physiological measures, and morning cortisol profiles. The primary outcome will be depressive and anxiety symptoms, measured by the Edinburgh Postnatal Depression Scale, the State Trait Anxiety Questionnaire, and the Pregnancy-Related Anxiety Questionnaire. Secondary outcomes include mindfulness, satisfaction with birth, quality of life, fetal attachment, bonding, mode of delivery, and cost-effectiveness. Discussion This is the first German RCT to examine the (cost-)effectiveness of an eMBI on maternal mental health during pregnancy. If successful, the mindmom app represents a low-threshold and cost-effective help for psychologically distressed women during pregnancy, thereby reducing the negative impact on perinatal health outcome. Trial registration Deutsches Register Klinischer Studien, German Clinical Trials Register DRKS00017210. Registered on 13 January 2020. Retrospectively registered.