The early childhood education and care (ECEC) environment is an important setting for providing children with daily opportunities for movement and music, supporting holistic child development in the early years. To date, there are no studies evaluating the implementation of a holistic programme in the ECEC context in the areas of movement behaviour and motor and musical skills. The main aim is to examine the effectiveness of a holistic movement and music programme on physical activity (PA), sedentary behaviour and sleep, motor skills and musical skills in young children (1–3 years). The secondary aims are to examine the impact of the movement and music programme on the perceptions of the educational community, as well as the barriers and facilitators they perceive in the process of baseline assessment, construction, and implementation of the movement and music programme in their own ECEC community. This cluster-randomised controlled trial (intervention and control groups) with public ECEC centres will be performed over a 24-month period. Baseline measurements will be taken in the first year of the project, and assessments to examine the effectiveness of the programme will take place 12 months after the baseline assessment. For young children the main outcome variables will be: (a) PA, sedentary time, and sleep time; (b) gross and fine motor skills; and (c) musical skills. The secondary outcomes will be: (a) PA and sedentary time during outdoor play and structured PA sessions; (b) play patterns during outdoor free play; and (c) movement and music behaviours after ECEC hours. For families, secondary outcomes will be: (a) perceived barriers and facilitators to PA in young children; (b) perceived barriers and facilitators to the inclusion of music at home; and (c) the means of transport to ECEC settings and barriers to active commuting. For ECEC educators, the secondary will be: (a) perceived barriers and facilitators for the inclusion of movement and music as curricular practices in the ECEC institution; (b) perceived impact of the implementation of the movement and music programme. This research project aims to fill a knowledge gap during a period of childhood that has rarely been explored, either nationally or internationally (1–3 years), and to position movement and music teaching practices as key contexts in the curriculum development of infant and toddler education.