Electrochemical fluorescence modulation of flavin redox centers covalently attached to a poly(allylamine)-hydrogel modified ITO electrode was achieved by faradaic modulation of redox states. At least a fraction of the fluorescent flavins is electroactive. Redox switching between oxidised flavin and non-fluorescent reduced leucoflavin was monitored by square wave modulated and linear scan voltfluorometry. Differential cyclic voltfluorograms and cyclic voltammograms are in very good agreement. In situ fluorescence spectroscopy can be applied to complement electrochemical studies of redox-dyes incorporated in polymeric matrices attached to the electrode surface. Advantages of electrochemical modulated fluorescence in these systems are enhanced sensitivity and selectivity in bio-sensors and the ability to obtain an insight into dynamic electron transfer processes.