Smallholder agriculture underpins most rural livelihoods and national economy in Tanzania and Malawi. Agricultural production by small holders in such countries is frustrated by several factors including climate change and variability (CC&V). Non agriculture community livelihoods activities and ecosystems are also negatively affected, adding costs to adaptation. The overall objective of the paper is sharing research experience on how climate change adaptation within agriculture sector can be strengthened using innovation approaches. Findings are based on a four years action research project funded by DFID through IDRC in Tanzania and Malawi. A total of 16 villages, 8 each in Tanzania and Malawi were involved and a Participatory Action Research was used. In total 360 farmers were initially involved in the project. Findings showed thas CC&V is affecting farming communities, institutions and organizations differently. Communities could adapt better if relevant information on climate and required products reaches them on time. Behaviour changes of different boundary partners like farmers, extension workers, agricultural based NGOs, stockists, media, with policy support (at both national and local levels) positively reduced vulnerabilities to CC&V and as a result sorghum, maize, beans and sunflower crop yields improved. For local innovation systems to work better a collective mobilisation of resources and collaboration of different boundary partners is required in this context .Adaptation program should focus more in supporting action oriented research or programs if capacity to adapt need to be strengthened in agricultural sector using innovative approaches.