Abstract Background Anaemia in pregnancy remains prevalent in Nepal and causes severe adverse health outcomes. Methods This non-blinded cluster-randomised controlled trial in the plains of Nepal has two study arms: (1) Control: routine antenatal care (ANC); (2) Home visiting, iron supplementation, Participatory Learning and Action (PLA) groups, plus routine ANC. Participants, including women in 54 non-contiguous clusters (mean 2582; range 1299–4865 population) in Southern Kapilbastu district, are eligible if they consent to menstrual monitoring, are resident, married, aged 13–49 years and able to respond to questions. After 1–2 missed menses and a positive pregnancy test, consenting women < 20 weeks’ gestation, who plan to reside locally for most of the pregnancy, enrol into trial follow-up. Interventions comprise two home-counselling visits (at 12–21 and 22–26 weeks’ gestation) with iron folic acid (IFA) supplement dosage tailored to women’s haemoglobin concentration, plus monthly PLA women’s group meetings using a dialogical problem-solving approach to engage pregnant women and their families. Home visits and PLA meetings will be facilitated by auxiliary nurse midwives. The hypothesis is as follows: Haemoglobin of women at 30 ± 2 weeks’ gestation is ≥ 0.4 g/dL higher in the intervention arm than in the control. A sample of 842 women (421 per arm, average 15.6 per cluster) will provide 88% power, assuming SD 1.2, ICC 0.09 and CV of cluster size 0.27. Outcomes are captured at 30 ± 2 weeks gestation. Primary outcome is haemoglobin concentration (g/dL). Secondary outcomes are as follows: anaemia prevalence (%), mid-upper arm circumference (cm), mean probability of micronutrient adequacy (MPA) and number of ANC visits at a health facility. Indicators to assess pathways to impact include number of IFA tablets consumed during pregnancy, intake of energy (kcal/day) and dietary iron (mg/day), a score of bioavailability-enhancing behaviours and recall of one nutrition knowledge indicator. Costs and cost-effectiveness of the intervention will be estimated from a provider perspective. Using constrained randomisation, we allocated clusters to study arms, ensuring similarity with respect to cluster size, ethnicity, religion and distance to a health facility. Analysis is by intention-to-treat at the individual level, using mixed-effects regression. Discussion Findings will inform Nepal government policy on approaches to increase adherence to IFA, improve diets and reduce anaemia in pregnancy. Trial registration ISRCTN 12272130.