Abstract* Background The high prevalence of infant stunting and maternal undernutrition in low- and middle-income countries poses a significant public health threat. The World Health Organization recommends balanced energy-protein (BEP) supplementation to pregnant women from populations with a high prevalence of underweight (prepregnancy BMI <18.5 kg/m2), leaving a notable gap in guidance for lactating women. Therefore, we established the Maternal BEP Studies Harmonization Initiative (BEP Initiative) to investigate the impact of BEP supplementation given to pregnant and/or lactating women on maternal and infant outcomes by synthesizing data from multiple clinical trials. This is a study protocol for our prospective individual participant data (IPD) meta-analysis on BEP lactation trials. Methods Data from four randomized controlled trials that include mother-infant dyads in India (n=816), Pakistan (n=957), Burkina Faso (n=800), and Nepal (n=726) will be pooled and analysed. Women were randomized to BEP (one trial had a third arm with maternal BEP plus infants receiving azithromycin) or control groups at baseline (during the first week) and received the intervention through six months postpartum. A one-stage IPD meta-analysis will be done using mixed-effects linear and log-binomial regression models to account for between-trial heterogeneity. The primary outcome of infant length-for-age z scores (LAZ) and secondary outcomes of maternal and infant indicators of nutritional status, all at six months of age, will be examined. Also, we will assess baseline characteristics as covariates and effect modifiers for the BEP to outcome relationship. Discussion This prospective IPD meta-analysis uses a one-stage IPD meta-analysis, which allows for higher statistical power to examine outcomes, more flexibility in defining variables, and can examine effect modifiers, which could inform which individuals or populations may benefit more from BEP given during lactation.