Fluorination of graphene enables tuning of its electronic properties, provided that control of the fluorination degree and of modification of graphene structure can be achieved. In this work we demonstrate that SF6 modulated plasma fluorination of monolayer graphene yields polyene-graphene hybrids. The extent of fluorination is determined by the plasma exposure time and controlled in real time by monitoring the change in the optical response by spectroscopic ellipsometry. Raman spectroscopy reveals the formation of polyenes in partially fluorinated graphene (F/C < 0.25), which are responsible for changes in conductivity and for opening a transport gap of ∼25 meV. We demonstrate that the cis- and trans-isomers of the polyenes in graphene are tunable using the photothermal switching. Specifically, the room temperature fluorination results in the cis-isomer that can be converted to the trans-isomer by annealing at T > 150 °C, whereas photoirradiation activates the trans-to-cis isomerization. The two isomers give to the polyene-graphene hybrids different optical and conductivity properties providing a way to engineer electrical response of graphene.