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In this article, we introduce a geometric and a spectral preorder relation on the class of weighted graphs with a magnetic potential. The first preorder is expressed through the existence of a graph homomorphism respecting the magnetic potential and fulfilling certain inequalities for the weights. The second preorder refers to the spectrum of the associated Laplacian of the magnetic weighted graph. These relations give a quantitative control of the effect of elementary and composite perturbations of the graph (deleting edges, contracting vertices, etc.) on the spectrum of the corresponding Laplacians, generalising interlacing of eigenvalues. We give several applications of the preorders: we show how to classify graphs according to these preorders and we prove the stability of certain eigenvalues in graphs with a maximal d-clique. Moreover, we show the monotonicity of the eigenvalues when passing to spanning subgraphs and the monotonicity of magnetic Cheeger constants with respect to the geometric preorder. Finally, we prove a refined procedure to detect spectral gaps in the spectrum of an infinite covering graph.