Different countries face diverse challenges for Conservation Agriculture (CA) development. The main purpose of this study was to examine the challenges of applying CA in Iran from the perspective of experts and farmers. A focus group method was used to investigate the challenges. The research sample consisting of farmers and experts of CA in different provinces includes those 19 experts and 15 farmers. Inductive content analysis and coding (open, axial, and selective coding) were employed to analyze the farmers’ and experts’ discussions. The findings showed that the challenges of applying CA in the studied provinces could be divided into 6 general categories: institutional-infrastructure (7 concepts), economic (5 concepts), training-research (2 concepts), environmental (4 concepts), mechanization (2 concepts), and cognitive (2 concepts) challenges. The economic and institutional-infrastructure challenges were the most frequent related to applying CA. It can be concluded that to solve the challenges of applying CA, it is necessary to link various sectors of government (the Ministry of Agriculture), education and research (Agricultural Research, Education and Extension Organization), and industry together. But farmers themselves are also a major contributor to meet the challenges of CA development through participation in planning CA project and training-extension programs. Therefore, farmers’ communities should also pave the way for a transition from conventional agriculture to CA with their participation.