A flame aerosol reactor (FLAR) was developed to synthesize nanoparticles with desired properties (crystal phase and size) that could be independently controlled. The methodology was demonstrated for TiO₂ nanoparticles, and this is the first time that large sets of samples with the same size but different crystal phases (six different ratios of anatase to rutile in this work) were synthesized. The degree of TiO₂ nanoparticle agglomeration was determined by comparing the primary particle size distribution measured by scanning electron microscopy (SEM) to the mobility-based particle size distribution measured by online scanning mobility particle spectrometry (SMPS). By controlling the flame aerosol reactor conditions, both spherical unagglomerated particles and highly agglomerated particles were produced. To produce monodisperse nanoparticles, a high throughput multi-stage differential mobility analyser (MDMA) was used in series with the flame aerosol reactor. Nearly monodisperse nanoparticles (geometric standard deviation less than 1.05) could be collected in sufficient mass quantities (of the order of 10 mg) in reasonable time (1 h) that could be used in other studies such as determination of functionality or biological effects as a function of size.