Numerous studies highlight the effectiveness of an integrated approach for the management of malaria, pneumonia and diarrhoea at the community level. There has however been little study on lessons learnt from implementation in practice and stakeholder experiences which could inform future programmatic planning and evaluation frameworks. A participatory, qualitative evaluation was conducted in the three varied settings of South Sudan, Uganda and Zambia, which have seen the scale up of integrated community case management (iCCM) over the last five years. All key in-country stakeholders were consulted on study design, with a particular focus on scope and methodology. Data collection methods included stakeholder consultations (key informant interviews, focus group discussions), and a review of project and Ministry of Health documentation. Data analysis followed the Framework Approach. Results suggest that iCCM implementation generally followed national pre-agreed guidelines. Overarching key programmatic recommendations included: collaboration with implementing partners in planning stages to positively impact on community acceptance and ownership; adoption of participatory training methods adapted to low literacy populations; development of alternative support supervision methods such as peer support groups; full integration of community level data into the health management information system and emphasizing data analysis, use and feedback at all levels; strengthened supply chains through improved quantification and procurement of commodities in conjunction with the national distribution network; community engagement to establish a support system for community health workers to increase their motivation; enhanced sensitisation and behaviour change communication to raise awareness and usage of appropriate health services; and advocacy at the national level for funding and logistical support for the continuation and integration of iCCM. This qualitative study is a valuable contribution in understanding the 'hows' of iCCM implementation with key insights for improved feasibility and acceptability. Main findings show how community support to iCCM and community health workers is necessary for sustained health benefits coupled with a focus on strengthening and 'enabling' the public health system. The participatory study design and methodologies used enabled the scope of the research enquiry to effectively capture various stakeholder perspectives.