Cobalt-substituted mixed spinel ferrites, used in various applications, have adjustable magnetic properties influenced by cation type and structural features. The theoretical framework for these materials assumes homogeneously magnetized, single-domain, non-interacting particles. However, recent studies reveal that nanoparticle systems are more complex, even with highly crystalline, monodisperse, non-interacting ensembles. Factors like spin disorder and dipolar interactions can significantly affect the material’s magnetic properties. In this study, we delve into the evolution of magnetic and structural properties within a series of oleate-capped manganese-substituted cobalt ferrites (denoted as Mn_xCo_1−xFe₂O₄) with varying Co/Mn molar ratios. The results can be interpreted solely based on their actual composition, independent of other parameters, thanks to the single-phase nanoparticles with similar crystallite and particle sizes (about 10 nm), size dispersity (14%), and weight percentage of capping oleate molecules (17%). The temperature and magnetic field dependences of the magnetization revealed magnetic anisotropy to be the key parameter affecting the magnetic parameters, including T_max, T_diff, T_b, H_c, H_K, and M_r/M_s, caused by different cobalt contents. Deviations from the ideal scenario of non-interacting NPs become evident in all samples when employing IRM-DCD protocols, showing negative ∆M peaks in Mn-rich samples (with a correlation between cobalt content and magnetic anisotropy), while positive ∆M is observed in the Co-enriched sample, possibly due to strong dipole–dipole interactions or surface spin phenomena. Small-Angle Polarized Neutron Scattering (SANSPOL) was then employed to study the quantitative distribution of magnetization within NPs, to reveal the presence of surface spin disorder, to access the surface anisotropy constant, and therefore to isolate the magnetocrystalline anisotropy and correlate it with the Mn content.