Superparamagnetic iron oxide nanoparticles are used in diverse applications, including optical magnetic recording, catalysts, gas sensors, targeted drug delivery, magnetic resonance imaging, and hyperthermic malignant cell therapy. Combustion synthesis of nanoparticles has significant advantages, including improved nanoparticle property control and commercial production rate capability with minimal post-processing. In the current study, superparamagnetic iron oxide nanoparticles were produced by flame synthesis using a coflow flame. The effect of flame configuration (diffusion and inverse diffusion), flame temperature, and additive loading on the final iron oxide nanoparticle morphology, elemental composition, and particle size were analyzed by transmission electron microscopy (TEM), high-resolution TEM (HR-TEM), energy dispersive spectroscopy (EDS), and Raman spectroscopy. The synthesized nanoparticles were primarily composed of two well known forms of iron oxide, namely hematite αFe2O3 and magnetite Fe3O4. We found that the synthesized nanoparticles were smaller (6–12 nm) for an inverse diffusion flame as compared to a diffusion flame configuration (50–60 nm) when CH4, O2, Ar, and N2 gas flow rates were kept constant. In order to investigate the effect of flame temperature, CH4, O2, Ar gas flow rates were kept constant, and N2 gas was added as a coolant to the system. TEM analysis of iron oxide nanoparticles synthesized using an inverse diffusion flame configuration with N2 cooling demonstrated that particles no larger than 50–60 nm in diameter can be grown, indicating that nanoparticles did not coalesce in the cooler flame. Raman spectroscopy showed that these nanoparticles were primarily magnetite, as opposed to the primarily hematite nanoparticles produced in the hot flame configuration. In order to understand the effect of additive loading on iron oxide nanoparticle morphology, an Ar stream carrying titanium-tetra-isopropoxide (TTIP) was flowed through the outer annulus along with the CH4 in the inverse diffusion flame configuration. When particles were synthesized in the presence of the TTIP additive, larger monodispersed individual particles (50–90 nm) were synthesized as observed by TEM. In this article, we show that iron oxide nanoparticles of varied morphology, composition, and size can be synthesized and controlled by varying flame configuration, flame temperature, and additive loading.