Background Families are a fundamental aspect in the current perspective of Early Intervention, and knowing their opinion with quantitative and qualitative research is necessary for its improvement. The objective of this research was to evaluate the quality of the service perceived in Early Intervention Centers and its relationship with satisfaction and future intention, as well as to identify factors that are associated with the perception of users. Methods A measurement model of 50 items and an open question to gather qualitative information was used in a sample of 233 participants. A confirmatory factor analysis and a regression analysis were conducted. Regarding the qualitative data, the information was subjected to a thematic content analysis in order to delve into the perception of the participants. Results The model showed a satisfactory fit and the regression analysis indicated that treatment rooms (β =  − 0.28) and adaptation of activities (β = 0.27) have greater weight with respect to satisfaction, whereas for future intention, the factors of greater weight were adaptation of activities (β = 0.23) and location (β = 0.20). The qualitative analysis showed three themes: facilitators, barriers and suggestions for improvement. Within facilitators, the participants were satisfied with the Early Intervention professionals, and they made improvement suggestions for the detected barriers to improve the facilities and the follow-up of the child. Conclusions The study offers a wide perspective of the perception of the service with an active participation of families in the treatment within the Early Intervention service. This will allow professionals in Early Intervention, service providers and researchers to consider the families as intervention agents capable of providing their opinion and making decisions, and not only as passive elements.