•Magnetic properties of GaAs:Mn nanostructures as a function of the Mn at. %.•Clusters role in the GaAs:Mn evolution from 2D to 3D growth mode.•AFM images showing directly the 2D to 3D transition in GaAs:Mn at high temperature.•Magnetic response of MnAs clusters related with GaAs:Mn surface structures.•Observation of an anomalous magnetic behavior related to confinement conditions. We report the influence of the Mn atomic concentration (at.%) on the nanostructures formation and magnetic properties of GaAs:Mn layers grown by Molecular Beam Epitaxy at a relatively high substrate temperature of 530 °C varying the nominal Mn at.% content from 0.01 to 0.2. It is shown that by modifying the Mn at.% different kind of nanostructures, ranging from 2D (such as islands and surface corrugation) to 3D microleave- and nanowire-like arrays, form on the surface layer. Samples produced with Mn contents ranging from 0.02 to 0.20 at.% show a significant room temperature ferromagnetic response that is attributed to the formation of MnAs nanocrystals as confirmed from X-ray diffraction analysis and magnetization measurements. The influence of MnAs clusters on the formation of the nanostructures observed is discussed.