This paper presents bioenergy value chain modelling to estimate the biomass and bioenergy cost of production and biomass netback in combined heat and power (CHP) systems. Modelling compares biomass cost and netback to analyse the feasibility of CHP systems, as well as the internal rate of return (IRR) and payback period (PBP). Models are implemented into the IMP Bio2Energy® software (Instituto Mexicano del Petróleo, Mexico City, Mexico) for practical application and demonstrated for bioenergy generation in the agroindustrial processes of tequila production, coffee and orange processing using as biomass the agave bagasse, coffee pulp and orange peels coproducts, respectively. Results show that the CHP systems are economically feasible, i.e., biomass cost of production is lower than netback, PBP between 3 and 4 years and IRR > 20%. The cost of bioenergy is lower than the cost of fuel oil and grid electricity being replaced. The sensitivity analysis for boiler steam pressure showed that there is an optimal pressure for coffee pulp (40 bar), a threshold pressure for orange (60 bar) and agave bagasse (70 bar). Sensitivity to biomass input indicated a maximum capacity where economy of scale does not produce any improvement in the indicators. Results demonstrate the usefulness of the modelling approach and IMP Bio2Energy® in analysing biomass CHP systems.