This paper presents a phase-shift control method for a converter containing a multi-winding transformer. The control strategy is developed from a power flow analysis of the converter and uses the derived power flow equations to supply constant power at a load port while the second load port experiences large load changes. This control method prevents the constant load port from experiencing transient behavior caused by magnetic coupling with the other load port. The approach is demonstrated with an experiment using a controller within a control hardware-in-theloop set-up and then a full experimental setup within a lower power test bed. By using control to mitigate the effects of mutual flux within a multi-winding transformer, the load ports of the converter are effectively decoupled. The analytical procedure described in this paper can also be applied to other converter topologies containing multi-winding transformers to achieve similar decoupled load performance, as demonstrated in the triple active bridge converter test bed.