Anaemia in children under five years remains a significant cause of mortality and morbidity in low-middle income countries. Globally, 27% of the world’s population is anaemic, of which developing countries account for more than 89%. The global prevalence is worse in Africa and Asia. Anaemia has the potential of maintaining the cycle of poverty, as it prevents children from attaining their full development potential. An important part of anaemia in children under-five years are preventable. Locally available dietary (LAD) interventions may be the sustainable interventions to address the high prevalence of anaemia in our communities. The aim of the study is to determine the effect of counselling on Locally Available Diet, on anaemia among children aged 6–59 months in the Kumbungu District of the Northern Region, Ghana. This study will be a community-based cluster randomized, controlled trial, with two parallel arms; Iron + Folic Acid (IFA arm) hereby referred to as the Standard care arm and Iron + Folic Acid + Counselling on Locally available dietary intervention (IFA+LAD arm) referred to as the Standard Plus arm. Study participants are children between the ages of 6 to 56 months. All study participants would receive iron plus folic acid. The minimum number of children per arm is 330 and the number of community clusters is 10 (5 per study arm). Also, considering this study proposes two parallel arms, the total minimum study sample size of children under five years is 496, the minimum total number of community clusters is 10 and a minimum of 25 households per community cluster, 124 households per study arm and 248 households for the study. Randomization is at the level of the clusters (selected communities). The intervention group receives counselling on LAD at a household level aimed at promoting the intake of locally available iron, folate and vitamin B12 rich foods. Also encourage the intake of food rich in enhancers of iron absorption and discouraging the intake of food rich in inhibitors of iron absorption. The primary outcome is mean haemoglobin levels in study arms. Secondary outcomes would include measurement of weight, height/length, mid upper arm circumference, dietary record, serum iron, ferritin, and other parameters of full blood count. Ethical clearance has been obtained and trial registered with Pan African Trial Registry (www.pactr.org) PACTR201906918438423.