In 2007 ANECCA was legally registered in Uganda as a not-for-profit company limited by guarantee and thus embarked on a process of organizational capacity development. Similar registration of ANECCA happened in Tanzania, Ethiopia, Nigeria, Niger and Burkina Faso.

In 2007, CRS/AIDSRelief provided support that was used to develop a paediatric and adolescent HIV counseling training package that was used to train service providers in Tanzania, Uganda, Kenya, Swaziland, and Zambia. This training package was later in 2018 improved with funding from the USAID AIDSFree Project into a Handbook on Counseling and Psychosocial Care for Children and Adolescents living with and affected by HIV in Africa.

In 2009 with support from USAID Ethiopia, ANECCA took the lead to scale up the paediatric HIV services through provision of technical support for comprehensive pediatric HIV & TB care, treatment and support at Health Centre level in five regions of Ethiopia. Between 2009 and 2011, 643 health care providers at 350 health centers were trained on pediatric HIV care, followed by monthly on-site clinical mentorship. The number of HIV-positive children enrolled in care at the 350 health centers increased from 1,447 in 2008 to 9,869 in 2011 and the number of children receiving ART increased from 48 to 3,763. From 2011 to 2014, ANECCA provided mentorship to health workers in health centers of Amhara and Tigray regions of Ethiopia with a USD 1,798,258 sub-grant from MSH under the USAID funded ENHAT-CS project.   In one year (October 2011 to September 2012) a total of 255 and 284 health workers were trained on comprehensive Paediatric training (IMNCI and Paediatric HIV) and PMTCT respectively in the 2 regions. Mentoring was done at 59 and 103 health centers in Tigray and Amhara respectively. Of the patients newly initiated on ART during the same period, 902 (8.8%) were children aged less than 15 years, that included 51 infants. The national target for children on ART was 10%.  In West Amhara, the proportion of Paediatric clients was 9.2% compared to 6.3% in East Amhara and 6.6%in Tigray. During the period October 2012 to September 2013, 479 intensive mentoring activities focusing on Paediatric HIV/AIDS were conducted at the 277 HCs in the Amhara and Tigray regions resulting in 1107 children (including 56 infants) being newly initiated on ART. From January 2012 to April 2013, ANECCA through a sub-grant from World Vision Ethiopia provided technical assistance to the Federal Ministry of Health in Ethiopia to scale up the Paediatric component of the national Preventive Care Package (PCP).

2010 and 2011 with funding from EGPAF, ANECCA conducted training of trainers and of service providers on psychosocial care and counseling HIV infected children and adolescents in Lesotho, Malawi, and Swaziland. ANECCA also provided Technical Assistance to MOH Swaziland to develop a national training curriculum for health care providers on HIV counseling and psychosocial support for children and adolescents.

In 2012 the secretariat moved out of RCQHC and thus ANECCA became independent of RCQHC and Makerere University.