A novel factorization-based, low-rank regularization method is introduced to solve multidimensional deconvolution (MDD) problems in the frequency domain. In this approach, each frequency component of the unknown wavefield is represented as a complex-valued square matrix and approximated as the product of a rectangular matrix and its transpose. The benefit of such a parameterization is twofold. First, each frequency matrix is guaranteed to be symmetric. From a physical standpoint, the recovered wavefield inherently adheres to the principle of reciprocity; in other words, the response to a receiver from a virtual source does not change when the two are swapped. Therefore, we refer to this low-rank parameterization as reciprocity-aware in that it respects the underlying physics of wave propagation associated with the MDD solution. Second, the size of the unknown matrix is greatly reduced compared with that of the original wavefield of interest (and halved compared with the existing factorization-based low-rank approximations). We further show that the associated objective function can be successfully optimized using the accelerated proximal gradient algorithm and present a robust strategy to define the initial guess of the solution. Numerical examples on synthetic and field data demonstrate the effectiveness of the proposed method in compressing the retrieved Green’s function while preserving its accuracy.