We define the open string version of the nonlinear sigma model on doubled geometry introduced by Hull and Reid-Edwards, and derive its boundary conditions. These conditions include the restriction of D-branes to maximally isotropic submanifolds as well as a compatibility condition with the Lie algebra structure on the doubled space. We demonstrate a systematic method to derive and classify D-branes from the boundary conditions, in terms of embeddings both in the doubled geometry and in the physical target space. We apply it to the doubled three-torus with constant H-flux and find D0-, D1-, and D2-branes, which we verify transform consistently under T-dualities mapping the system to f -, Q-and R-flux backgrounds.We also require the Neumann projector to be integrable, so that it locally defines the brane as a smooth submanifold of the target space,The projectors are moreover required to be orthogonal with respect to the doubled metric M IJ , 0 = Ξ I K M IJ Ξ