Background The aim of this study was to compare bran yields of short- and long-flow roller mill from biofortified (+) and nonbiofortified (-) hull-less oats cv. Haskara and determine effect of biofortification (Zn, I, Se) on composition and physicochemical properties of fractions. Findings Zn, I, and Se contents were significantly increased by biofortification. Yields of coarse bran (CB) obtained by short flow were 42.6% for both Haskara samples, while those of fine bran (FB) obtained by long flow were 46.6% and 47.4% for Haskara (+) and Haskara (-). Beta-glucan (BG) contents of CB were 8.42% and 8.31%, while those of FB were 8.68% and 8.65% for respective samples. There were no significant differences between CB of Haskara (+) and Haskara (-) samples in terms of mass median diameter, dispersion, particle density, porosity, BG solubility, and RVA viscosity. The differences between FB of the same samples were also not significant in terms of those parameters. However, long flow significantly increased dispersion, porosity, BG solubility, and RVA viscosity and significantly decreased mass median diameter and bulk density compared to short flow. Conclusions Biofortified oats can be used to obtain beta-glucan-enriched milling fractions. Significance and novelty This is the first study on bran fractions obtained by different milling flows from biofortified hull-less oats.