The Healthy Life Trajectories Initiative, an international consortium developed in partnership with the World Health Organization, is addressing childhood obesity from a life-course perspective. It hypothesises that an integrated complex intervention from preconception, through pregnancy, infancy and early childhood, will reduce childhood adiposity and non-communicable disease risk, and improve child development. As part of the Healthy Life Trajectories Initiative in South Africa, the Bukhali randomised controlled trial is being conducted with 18–28-year-old women in Soweto, where young women face numerous challenges to their physical and mental health. The aims of this paper were to describe the intervention development process (including adaptations), intervention components, and process evaluation; and to highlight key lessons learned. Intervention materials have been developed according to the life-course stages: preconception (Bukhali), pregnancy (Bukhali Baby), infancy (Bukhali Nana; birth—2 years), and early childhood (Bukhali Mntwana, 2–5 years). The intervention is delivered by community health workers, and includes the provision of health literacy resources, multi-micronutrient supplementation, in-person health screening, services and referral, nutrition risk support, SMS-reminders and telephonic contacts to assist with behaviour change goals. A key adaption is the incorporation of principles of trauma-information care, given the mental health challenges faced by participants. The Bukhali process evaluation is focussing on context, implementation and mechanisms of impact, using a mixed methods approach. Although the completion of the trial is still a number of years away, the documentation of the intervention development process and process evaluation of the trial can provide lessons for the development, implementation, and evaluation of such complex life-course trials.