A quartz tube with inner wall contaminated by Escherichia coli bacteria is treated using an atmospheric pressure nitrogen afterglow flowing at 20 SLM. The biocidal efficacy is measured locally at both the input and at the output of a 57 cm tube, giving a reduction of survivors of around 5 and 4 log for a 40 min treatment time, respectively. A weak contribution of gas heating is observed and delineated from the effect uniquely due to the plasma afterglow. Based on previous work, a model allows the estimation of the variation of the axial concentration of N atoms, assumed to be the main active species, and its correlation to the biocidal effect of the afterglow. Extrapolation of the model opens the perspective of the decontamination of longer tubes with smaller diameters such as catheter and endoscope ducts.