The study investigated methodological approaches to economic crises and characterised crisis phenomena in the economy. The reasons for the development of the crisis in agriculture are considered and the prerequisites for the exit of the agro-industrial complex from the crisis are systematised. The factors of increasing the instability of the agricultural sector in the context of the global economic crisis are analysed. The study highlighted a set of circumstances that determine the negative and positive effects of the crisis, as well as the prerequisites for overcoming it. Without their consideration, it is difficult to objectively determine the probable losses and predict potential options for the development of the agro-industrial complex in Kazakhstan. Based on a comparative analysis of existing approaches to economic crises, special attention was paid to the structural crisis. A method for diagnosing crisis phenomena in the agricultural sector of Kazakhstan was developed, which constitutes a set of methods and techniques that allow establishing and studying alarming conditions in the agricultural sector to predict and prevent them in the future. It was concluded that the situation in the agricultural sector does not fall within the conventional classification of economic crises and it was proposed to supplement the methods for assessing periodic crises by including a systemic crisis.