Background: Iron deficiency (ID) and iron deficiency anaemia (IDA) have global and severe health implications, and disproportionately impact women of reproductive age. Current methods of supplementing diets with iron are challenged by poor adherence and palatability, reducing effectiveness of these treatment strategies. The aim of this study is to evaluate the efficacy of a novel home beverage fortification with a mineral-enriched powder, designed to enhance bioavailability and ease of use, for the treatment of ID in women of reproductive age. Methods: This single-centre, randomised, double-blinded placebo-controlled trial will enrol 150 eligible biologically female participants with ID. Participants will be randomly assigned to the active intervention (iron/zinc-enriched powder) or control group (placebo powder) over 6 months. Primary outcomes will include change in serum ferritin (SF) concentrations and proportion of participants who remain iron deficient at 6-months. Secondary outcomes will include change in SF and haemoglobin (Hb) concentrations across timepoints, and levels of metabolites and key circulating pro-inflammatory biomarkers, changes in dietary intakes, self-reported perceptions of health, barriers to use of the powder, adherence and palatability, safety outcomes, and cost-effectiveness. Exploratory outcomes will assess the gut microbial metagenome and metabolome. Discussion: Fortification, an effective approach for the prevention of ID/IDA, has advantages over some methods of supplementation because it uses low levels of iron, minimising unpleasant side effects, does not risk toxicity, and has high acceptability and compliance rates. This mineral-enriched powder uses electrolytic iron and zinc sulphate monohydrate of a small particle size, which is less irritating to the gut, and facilitates bioavailability. Findings from the study will be shared with those affected by and involved in treating these conditions, as a novel intervention that is both effective and acceptable among women of reproductive age would help to improve treatment compliance, and ultimately, reduce ID/IDA burden. Trial registration: This trial is registered at clinicaltrials.gov (NCT05990166): https://clinicaltrials.gov/study/NCT05990166, August 2023.