This paper presents the first realization of a simultaneous 87Rb-85Rb Mach-Zehnder atom interferometer with Bose-condensed atoms. A number of ambitious proposals for precise terrestrial and space based tests of the weak equivalence principle rely on such a system. This implementation utilizes hybrid magnetic-optical trapping to produce spatially overlapped condensates with a repetition rate of 20 s. A horizontal optical waveguide with co-linear Bragg beamsplitters and mirrors is used to simultaneously address both isotopes in the interferometer. We observe a non–linear phase shift on a non-interacting 85Rb interferometer as a function of interferometer time, T, which we show arises from inter-isotope scattering with the co-incident 85Rb interferometer. A discussion of implications for future experiments is given.