Iterative learning control (ILC) is a powerful technique to regulate repetitive systems. Additive manufacturing falls into this category by nature of its repetitive action in building three-dimensional structures in a layer-by-layer manner. In literature, spatial ILC (SILC) has been used in conjunction with additive processes to regulate single-layer structures with only one class of material. However, SILC has the unexplored potential to regulate additive manufacturing structures with multiple build materials in a three-dimensional fashion. Estimating the appropriate feedforward signal in these structures can be challenging due to iteration varying initial conditions, system parameters, and surface interaction dynamics in different layers of multi-material structures. In this paper, SILC is used as a recursive control strategy to iteratively construct the feedforward signal to improve part quality of 3D structures that consist of at least two materials in a layer-by-layer manner. The system dynamics are approximated by discrete 2D spatial convolution using kernels that incorporate in-layer and layer-to-layer variations. We leverage the existing SILC models in literature and extend them to account for the iteration varying uncertainties in the plant model to capture a more reliable representation of the multi-material additive process. The feasibility of the proposed diagonal framework was demonstrated using simulation results of an electrohydrodynamic jet printing (e-jet) printing process.