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The energy crisis and environmental pollution are serious challenges that humanity will face for the long-term. Despite tremendous efforts, the development of environmentally friendly methods to fabricate new energy materials is still challenging. Here we report, for the first time, a new strategy to fabricate various doped carbon nanofiber (CNF) aerogels by pyrolysis of bacterial cellulose (BC) pellicles which had adsorbed or were dyed with different toxic organic dyes. The proposed strategy makes it possible to remove the toxic dyes from waste-water and then synthesize doped CNF aerogels using the dyed BC pellicles as precursors. Compared with other reported processes for preparing heteroatom doped carbon (HDC) nanomaterials, the present synthetic method has some significant advantages, such as being green, general, low-cost and easily scalable. Moreover, the as-prepared doped CNF aerogels exhibit great potential as electrocatalysts for the oxygen reduction reaction (ORR) and as electrode materials for supercapacitors.