Magnetocrystalline anisotropy is a key parameter governing the performance of magnetic nanoparticles in many applications. However, disentangling its intrinsic contribution from other sources of effective anisotropy, such as surface effects, dipolar interactions or shape anisotropy, remains highly challenging. Here, we report a novel approach to qualitatively estimate the magnetocrystalline anisotropy of two CoxFe3−xO4 nanoparticles with different Co contents (x = 0.11 and 0.61) using polarized neutron powder diffraction (PNPD). The off-diagonal elements of the susceptibility tensors and degree of asymmetry of the magnetization ellipsoids obtained from the PNPD refinements reveal that the sample with x = 0.61 presents a larger magnetocrystalline anisotropy than the sample with x = 0.11, which is consistent with the effective anisotropy derived from magnetometry. Moreover, comparison of the PNPD-derived magnetization ellipsoids across materials with varying anisotropies confirms the direct relationship between the ellipsoid asymmetry and magnetocrystalline anisotropy. These findings establish PNPD as a powerful tool for qualitatively probing intrinsic anisotropies in nanoparticle systems, paving the way for the rational design and optimization of magnetic nanoparticles for advanced applications.