This article traces the clash between individual agency and organizational structures characterising the Egyptian Muslim Brotherhood in the aftermath of the 2013 coup, identifying these tensions as a main point of contention driving its internal restructuring. Since Mohammed Morsi’s violent toppling the Brotherhood experienced a process of gradual fragmentation, with tensions developing between different approaches to repression. To provide a clearer picture of the internal challenges facing the Brotherhood today, this article traces the clash between agency and structure within the organization – understood as the emergence of members’ own subjectivities and initiatives vis-a-vis the movement’s organizational structures and collective identity – from 2011 to the post-2013 context . It argues that these tensions are at the core of the organization’s fragmentation in the aftermath of the 2013 coup and that they pre-date the new dimension of exile, as they are embedded in the very principles over which the Brotherhood historically rests. The article aligns with an emerging trend in the literature on the Brotherhood that places the attention on how members themselves engage with identity and ideological questions, develop strategies to move forward, and on their role in driving processes of change within the movement. Therefore, it showcases primary data obtained through over 30 semi-structured interviews conducted with former and current Brotherhood members from across the organizational spectrum, and through several rounds of ethnographic fieldwork that took place in Turkey and the UK between 2013 and 2019. In particular, this article focuses on the analysis of the members’ individual experiences, aiming to go beyond the examination of the Brotherhood as a monolithic movement. By doing so, the article argues for the adoption of a new lens through which to approach the study of the organization in the post 2013 context, taking into accounts its changed circumstances and focusing on the relationship between the movement and its members to make sense of its current trajectories and transformation. Overall, it shows that the ongoing clash between individual agency and organizational structures is directly challenging the Brotherhood’s core principles, initiating a process of internal change that is likely to drastically reshape the aim and scope of the movement going forward.