The layered 5d transition metal oxide Sr2IrO4 has been shown to host a novel Jeff=1/2 Mott spin orbit insulating state with antiferromagnetic ordering, leading to comparisons with the layered cuprates. Here we study the effect of substituting Mn for Ir in single crystals of Sr2Ir0.9Mn0.1O4 through an investigation involving bulk measurements and resonant x-ray and neutron scattering. We observe a new long range magnetic structure emerge upon doping through a reordering of the spins from the basal plane to the c-axis with a reduced ordering temperature compared to Sr2IrO4. The strong enhancement of the magnetic x-ray scattering intensity at the L3 edge relative to the L2 edge indicates that the Jeff=1/2 state is robust and capable of hosting a variety of ground states.