Quantum sensors based on cold atoms are being developed which produce measurements of unprecedented accuracy. Due to shifts in atomic energy levels, quantum sensors often have stringent requirements on their internal magnetic field environment. Typically, background magnetic fields are attenuated using high permeability magnetic shielding, with the cancelling of residual and introduction of quantisation fields implemented with coils inside the shield. The high permeability shield, however, distorts all magnetic fields, including those generated inside the sensor. Here, we demonstrate a solution by designing multiple coils overlaid on a 3D-printed former to generate three uniform and three constant linear gradient magnetic fields inside the capped cylindrical magnetic shield of a cold atom interferometer. The fields are characterised in-situ and match their desired forms to high accuracy. For example, the uniform transverse field, Bx, deviates by less than 0.2% over more than 40% of the length of the shield. We also map the field directly using the cold atoms and investigate the potential of the coil system to reduce bias from the quadratic Zeeman effect. This coil design technology enables targeted field compensation over large spatial volumes and has the potential to reduce systematic shifts and noise in numerous cold atom systems.