The microstructural transitions of aggregated magnetic inks under shear flow were characterized using a microstructure-based model and validated by experimental data. To describe the shear-dependent viscosity and structural dynamics, an elastic floc model was developed within the context of weakly aggregated dispersions. This approach enabled the determination of aggregate dimensions relative to the applied shear rate, providing insight into the structural response of magnetic inks. Findings indicate that floc size is inversely proportional to the particle volume fraction, yet it is surprisingly insensitive to long-range magnetic interactions. We report two shear-induced yielding regimes: the first corresponds to the breakage of the network’s physical connectivity, where inter-floc interactions maintain a residual framework, while the second corresponds to the total rupture of flocs. A comparison of the steady and dynamic shear measurements suggests that the linear viscoelastic region is fundamentally limited by the secondary yielding threshold. This model provides a comprehensive understanding of shear thinning as a synergistic effect of floc deformation and disintegration.