Two samples of double-walled carbon nanotubes (DWCNTs), one with well-graphitized nanotube walls and another containing oxygen at outer nanotube surfaces, were fluorinated at room temperature using gaseous BrF3. The products were comprehensively studied using transmission electron microscopy, Raman scattering, X-ray photoelectron, and near-edge X-ray absorption fine structure spectroscopies. The experimental data found twice the concentration of sidewall fluorine in the oxygenated DWCNTs. Quantum chemical modeling supported the experimental results revealing the preferable development of CF areas near the carbon atoms bonded with oxygen-containing groups. This observation demonstrates that tuning of the physical and chemical properties of carbon nanotubes can be achieved via the controlled co-modification by fluorine and oxygen functional groups.