The magnetic response of nanostructures plays an important role on biomedical applications being strongly influenced by the magnetic anisotropy. In this work, we investigate the role of the temperature, particle concentration and nanoparticles arrangement forming aggregates in the effective magnetic anisotropy of Mn-Zn ferrite-based nanoparticles. Electron magnetic resonance and coercivity temperature dependence analyses, were critically compared for the estimation of the anisotropy. We found that the temperature dependence of the anisotropy follows the Zener-Callen model, while the symmetry depends on the particle concentration. At low concentration one observes only an uniaxial term, while increasing a cubic contribution has to be added. The effective anisotropy was found to increase the higher the particle concentration on magnetic colloids, as long as the easy axis was at the same direction of the nanoparticle chain. Increasing even further the concentration up to a highly packed condition (powder sample) one observes a decrease of the anisotropy, that was attributed to the random anisotropy axes. Further, room temperature anisotropy decreased on the order of 50% in comparison to the low temperature values, thus impacting the theoretical estimations of the magnetic response of nanoparticles.