Spectral domain optical coherence tomography (SD-OCT) is a highly versatile method which allows for three dimensional optical imaging in scattering media. A number of recent publications demonstrated the technique to benefit from structured illumination and beam shaping approaches, e.g. to enhance the signal-to-noise ratio or the penetration depth with samples such as biological tissue. We present a compact and easy to implement design for independent wavefront manipulation and beam shaping at the reference and sample arm of the interferometric OCT device. The design requires a single spatial light modulator and can be integrated to existing free space SD-OCT systems by modifying the source arm only. We provide analytical and numerical discussion of the presented design as well as experimental data confirming the theoretical analysis. The system is highly versatile and lends itself for applications where independent phase or wavefront control is required. We demonstrate the system to be used for wavefront sensorless adaptive optics as well as for iterative optical wavefront shaping for OCT signal enhancement in strongly scattering media. © 2019, The Author(s).