The national curriculum for early childhood education allows ECEC institutions to apply alternative pedagogy. Some of the privately owned ECEC institutions use alternative pedagogical methods that correspond to the institution's general approach (Waldorf-preschools, Christian ECEC institutions, etc.). The most widespread methodologies put into practice in preschool child care institutions are the so-called StepbyStep Methodology, Reggio Emilia approach and Montessori approach, the environment of which allows also the application of other active teaching methodologies (discovery learning).

Alternative pedagogy is also implemented in ECEC institutions for children with special needs. Pedagogues are responsible for the effectiveness of the methods of instruction they use.

Among private ECEC institutions, also English language based ECEC institutions exist (for children of the international community).

Since the 1st of September 2024, educational activities in ECEC institutions take place in the Estonian language. Establishing Estonian as the language of instruction in ECEC is part of the transition to Estonian-medium education in kindergartens and schools with another language of instruction. The language of instruction can be different from Estonian only in private kindergartens and municipal kindergartens based on a special government permit.

Estonian-medium kindergartens must support the acquisition of the Estonian language of children with a different home language through integrated learning and educational activities and, if necessary, specific language learning activities.