Removing organics from hybrid nanostructures is a crucial step in many bottom-up materials fabrication approaches. It is usually assumed that calcination is an effective solution to this problem, especially for thin films. This assumption has led to its application in thousands of papers. We here show that this general assumption is incorrect by using a relevant and highly controlled model system consisting of thin films of ligand-capped ZrO2 nanocrystals. After calcination at 800 °C for 12 h, while Raman spectroscopy fails to detect the ligands after calcination, elastic backscattering spectrometry characterization demonstrates that ~18% of the original carbon atoms are still present in the film. By comparison plasma processing successfully removes the ligands. Our growth kinetic analysis shows that the calcined materials have significantly different interfacial properties than the plasma-processed counterparts. Calcination is not a reliable strategy for the production of single-phase all-inorganic materials from colloidal nanoparticles.