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Abstract Background Antenatal balanced energy and protein (BEP) supplements have well-documented benefits for pregnancy outcomes. However, considerable practical gaps remain in the effective and cost-effective delivery of antenatal BEP supplements at scale in low- and middle-income countries. Methods A randomized effectiveness study will be conducted in two sub-cities of Addis Ababa, Ethiopia, to evaluate the effectiveness, cost-effectiveness, and implementation of different targeting strategies of antenatal BEP supplements. Pregnant women aged 18 to 49, with a gestational age of 24 weeks or less, and attending antenatal visits in one of the nine study health facilities are eligible for enrollment. In six of the health facilities, participants will be randomized to one of three study arms: control (Arm 1), targeted BEP provision based on baseline nutritional status (Arm 2), and targeted BEP supplementation based on baseline nutritional status and monthly gestational weight gain (GWG) monitoring (Arm 3). In the remaining three facilities, participants will be assigned to universal BEP provision (Arm 4). Participants in Arms 2 and 3 will receive BEP supplements if they have undernutrition at enrollment, as defined by a baseline body mass index less than 18.5 kg/m2 or mid-upper arm circumference less than 23 cm. In Arm 3, in addition to targeting based on baseline undernutrition, regular weight measurements will be used to identify insufficient GWG and inform the initiation of additional BEP supplements. Participants in Arm 4 will receive BEP supplements until the end of pregnancy, regardless of baseline nutritional status or GWG. All participants will receive standard antenatal care, including iron and folic acid supplementation. A total of 5400 pregnant women will be enrolled, with 1350 participants in each arm. Participants will be followed up monthly during their visits to the antenatal facilities until delivery. Maternal and infant health status will be evaluated within 72 h after delivery and at 6 weeks postpartum. The effectiveness and cost-effectiveness of the different BEP targeting strategies in preventing adverse pregnancy outcomes will be compared across arms. Qualitative data will be analyzed to assess the feasibility, acceptability, and implementation of different supplementation strategies. Discussion This study will inform global recommendations and operational guidelines for the effective and cost-effective delivery of antenatal BEP supplements. The targeted approaches have the potential for broader scale-up in Ethiopia and other low-resource settings with a high burden of undernutrition among pregnant women. Trial registration ClinicalTrials.gov registration number: NCT06125860. Registered November 9, 2023.