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Fragmenting security sectors are a common mechanism of “coup-proofing” by state leaders. Multiple armed organizations can serve as counter-balances to the regular military, and multiple chains of command in the coercive sector can present coordination obstacles to coup-plotters. Less understood, however, are the implications of this fragmentation for other elements of conflict processes. Drawing on the literature on rebel group fragmentation, I argue that security sector fragmentation on the government side can lengthen civil wars and disrupt peace processes. While complex chains of command and multiple autonomous units can help fortify states against coups, they also increase the number of veto points at which a peace process can be disrupted and make “spoilers” to fragile peace more likely. In contrast, centralized chains of commands and cohesive security sectors allow states to ensure that peace agreements and ceasefires are obeyed on the government side. I test these expectations using data on civil war duration, peace agreements, and the fragmentation of security sectors and chains of command.