Agricultural transformation agenda among other things aims at making Nigeria food secure. This mission stands to be threatened by the negative impact of climate change, hence, innovations that will help overcome the threats is paramount. Such innovations could be developed in the universities if the needed enabling environment is provided. This study examines the capabilities of universities in combating the problems of climate change towards increased food production. A total sample size of 79 respondents selected from universities in Southeast, Nigeria was used. Data were collected with the use of questionnaire and analysed using descriptive and inferential statistics including percentage and factor analysis. All (100%) the respondents had no capability in acquiring machines and equipment needed for teaching and conducting researches on climate change. Majority (85%) of the respondents had no capability in terms of human resource development with regards to climate change. Funding/manpower, organisational and weak policy related factors influenced the development of the capabilities of the respondents. For a successful agricultural transformation that will not be marred by the negative impact of climate change, the study recommends that the Federal Government of Nigeria should provide adequate funding to the universities in order to enhance the development of their capabilities in acquiring machines and other things needed for the teaching and research in climate change related issues. Also, bodies concerned should provide regular in-service training for respondents in other to promote human resource needed for tackling climate change issues.