This paper deals with an economic comparison between costs and incomes in small wastewater treatment plants where the anaerobic co-digestion process of sludge and biowaste with energy recovery is operated. Plants in the size range 1,000–30,000 persons equivalent (pe) were considered in the study: typical costs, comprehensive of capital and operating costs, were in the range €69–105 per person per year depending on the plant size: the smaller the size the higher the specific cost. The incomes deriving from taxes and fees for wastewater treatment are generally in the range €36–54 per person per year and can only partially cover costs in small wastewater treatment plants. However, the co-treatment of biowaste and the use of produced energy for extra credits (green certificates) determine a clear improvement in the possible revenues from the plant. These were calculated to be €23–25 per person per year; as a consequence the costs and incomes can be considered comparable for wastewater treatment plants (WWTPs) with size larger than 10,000 pe. Therefore, anaerobic co-digestion of biowaste and sludge can also be considered a sustainable solution for small wastewater treatment plants in rural areas where several different kinds of biowaste are available to enhance biogas production in anaerobic reactors.