In this study, electrochemical oxidation of five azo dyestuffs (Yellow D-5GN, Red D-B8, Ruby F-2B, Blue D-5RN, Black DN), that are widely used in the textile industry, was investigated in a flow reactor. BDD electrode with a high boron doping level (C/B = 10 000) was prepared and used. Two configurations of reactor were considered, i.e., one with the undivided cell, and the other with the cell divided by anodic and cathodic compartments. The effect of current density and the initial pH of the solution on the dyestuff degradation process was investigated. As expected, higher degradation rate was found for higher current density, while the effect of pH was marginal. Next, electrochemical oxidation of azo dyestuffs with different chemical structures was investigated. Based on the cyclic voltammetry measurements, the correlation between the dyestuff removal rate and the oxidation potential value of dyestuff was found. These results suggest that the direct oxidation of dyestuffs at the highly doped BDD anode plays a significant role in the electrochemical oxidation. Finally, the electrochemical removal of dyestuffs was carried out in two types of dyeing baths. The dyeing bath composition has a significant effect on the degradation efficiency. Chlorides in F-type dyeing bath accelerated electrochemical removal due to effective generation of Cl2/HOCl at the highly B-doped BDD anode. In contrast, OH− inhibited the D-type dyestuff removal from dyeing bath, because they acted as scavengers of ·OH radicals. Highly B-doped BDD anode is promising material to F-type dyestuff treatment in industrial wastewater.