Doped SrTiO3 thin films, 55 nm thick, were epitaxially grown by Pulsed Laser Deposition with niobium contents ranging from 2 to 5 mol% on SrTiO3 and LaAlO3 substrates. The different templates result in different growth defects, film growth mechanism and therefore a different volume fraction of uniformly strained film under the critical thickness. The investigation of the conductivity reveals a significant difference between the two substrate choices, but only at elevated temperatures with conductivity values up to 30% larger for films on SrTiO3 substrates compared with LaAlO3. Whereas in bulk ceramics the niobium level dictates the total conductivity, here it was found that the substrate choice had a greater influence for thin films, in particular at temperatures over 400 C. This finding provides important information on conductive layers in complex heterostructures where strain and defects could work cooperatively. © 2013 Elsevier B.V. All rights reserved.