We present control schemes for open quantum systems that combine decoupling and universal control methods with coding procedures. By exploiting a general algebraic approach, we show how appropriate encodings of quantum states result in obtaining universal control over dynamically-generated noise-protected subsystems with limited control resources. In particular, we provide an efficient scheme for performing universal encoded quantum computation in a wide class of systems subjected to linear non-Markovian quantum noise and supporting Heisenberg-type internal Hamiltonians.