The synthesis of a complex hierarchical nanostructure with a definite number density and crystallite/cluster size is very challenging. Here we report a novel strategy to produce spherical magnetic colloidal nanocrystal clusters (Ni-doped iron oxide) of varying sizes using a thermosensitive polymer soft template through a hydrothermal approach. The magnetic colloidal nanocrystal clusters are nucleated in the globular spherical templates formed in the thermosensitive polymer; poly(N-isopropyl acrylamide), above lower critical solution temperature (LCST) where it acts as a nucleating agent in the initial stage and as a capping agent later. When the solution reaches super-saturation during the nucleation stage, the Ni2+, Fe2+ and Fe3+ hydroxides precipitate as ferrites of critical size and get attached to the PNIPAM globule through the coordination of oxygen and nitrogen. It was observed that, after the addition of Ni2+ ions, non-stoichiometric Ni ferrites nanocrystals were formed whereas the hematite phase was formed in the absence of Ni doping. XPS results show the presence of cation vacancies due to oxidation of Ni2+ and Fe2+. We also studied the adsorption/desorption of an anionic cefixime drug, conjugated on nanoclusters, above and below the lower critical solution temperature. The cefixime adsorption studies on the clusters showed that ~70 g/L of the sample is required to obtain a 66 sorption% at 25 °C and 52 sorption% at 45 °C. The percentage of cefixime sorption after the five cycles of regeneration was ~70%. The dye adsorption studies reveal that 15 g/L of the sample showed 99% sorption% of methylene blue at 25 °C and 87% sorption% at 45 °C This approach can be used as a new strategy to achieve controlled recovery of adsorbates (antibiotics and dyes) from aqueous solutions.