This study investigates the formation of by-product species during flame spray synthesis (SFS) of superparamagnetic maghemite (γ-Fe₂O₃) nanoparticles. Four samples are synthesized by utilizing two standardized burner types (SpraySyn1 and SpraySyn2) and varying the iron (III) nonahydrate (INN) concentration (0.1 M and 0.2 M) in the precursor feed while using ethanol and 2-ethylhexanoic acid as solvent. Conducting complementary powder analysis revealed a predominant presence of carboxylates and carbonates as by-product species (~14–18 wt.%), while no strong indications for elemental carbon and precursor/solvent residues can be found. Carbonates/carboxylates are located on particle surfaces, and the particles’ surface loadings by these species are independent of the precursor concentration but depend on burner type, with SpraySyn2 exhibiting lower values, indicating a more complete combustion for this burner. Through time-resolved thermophoretic sampling, we further demonstrate that carbon forms temporally in the visible flame center when using SpraySyn1. Since carbon solely forms momentarily within large flame pulses and decomposes further downstream, its temporal formation is of minor relevance for the final particle purity. However, its local co-existence aside from γ-Fe₂O₃ in the flame has potential to bias in situ diagnostics.