Under the terms of the Creative Commons Attribution (CC BY) license to their work. ; A route to engineer the intrinsic colossal magnetoresistance (CMR) response in manganite thin films through an accurate control of the growth kinetics is presented. It is shown that under specific growth conditions, a particular strained state, substantially different from that of bulk-like materials and standard films, can be quenched up to film thicknesses around 60 nm. This strained state exhibits the same structural fingerprints of the interfacial dead layer in standard films and promotes surface morphology instabilities, which end up with the formation of self-organized nanopits array. At the same time, it has profound effects on the intrinsic magnetoelectronic properties of the films that exhibit an enhanced intrinsic CMR response. ; We acknowledge financial support from the Spanish MEC (MAT2011-29081 and MAT2012-33207), CONSOLIDER (CSD2007-00041), and FEDER program. Z.K. thanks the Spanish MINECO for the financial support through the RyC program. We thank Helmholtz-Zentrum Berlin for the allocation of neutron/synchrotron radiation beamtime. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement No. 312284. ; Peer Reviewed