Inspired by the microscopic control over dissipative processes in quantum optics and cold atoms, we develop an open-system framework to study dissipative control of transport in strongly interacting fermionic systems, relevant for both solid state and cold atom experiments. We show how subgap currents exhibiting Multiple Andreev Reflections -the stimulated transport of electrons in the presence of Cooper-pairs -can be controlled via engineering of superconducting leads or superfluid atomic gases. Our approach incorporates dissipation within the channel, which is naturally occurring and can be engineered in cold gas experiments. This opens opportunities for engineering many phenomena with transport in strongly interacting systems. As examples, we consider particle loss and dephasing, and note different behaviour for currents with different microscopic origin. We also show how to induce nonreciprocal electron and Cooper-pair currents.Introduction. Understanding and controlling the outof-equilibrium dynamics of strongly interacting manybody systems constitutes one of the key forefronts in quantum physics across a variety of subfields in experiment and theory. In this context, opportunities to achieve their control via dissipation mechanisms have arisen [1,2], as is applied for few-body systems in quantum optics [3,4]. This is especially true in cold-atom platforms, where large separations between frequency scales allows well-controlled theoretical models and implementations of dissipative processes, as realized for laser cooling and trapping [5]. The longer timescales of cold atom experiments also allow dynamics to be tracked and potentially controlled time-dependently [6,7]. Outof-equilibrium transport dynamics remain a ubiquitous paradigm in the solid state [8], and recent developments in cold atom systems have also made it possible to engineer quantised transport of atoms between reservoirs, as well as quantum point contacts and waveguides [9][10][11][12]. Here we explore the emerging new opportunity of using dissipation engineering to achieve control of quantum transport properties, that are relevant for both coldatom and solid-state platforms.