In light of possible future restrictions on the use of fossil fuel, due to climate change obligations and continuous depletion of global fossil fuel reserves, the search for alternative renewable energy sources is expected to be an issue of great concern for policy stakeholders. This study assessed the feasibility of bioenergy production under relatively low-intensity conservative, eco-agricultural settings (as opposed to those produced under high-intensity, fossil fuel based industrialized agriculture). Estimates of the net energy gain (NEG) and the energy return on energy invested (EROEI) obtained from a life cycle inventory of the energy inputs and outputs involved reveal that the energy efficiency of bioenergy produced in low-intensity eco-agricultural systems could be as much as much as 448.5–488.3 GJ·ha−1 of NEG and an EROEI of 5.4–5.9 for maize ethanol production systems, and as much as 155.0–283.9 GJ·ha−1 of NEG and an EROEI of 14.7–22.4 for maize biogas production systems. This is substantially higher than for industrialized agriculture with a NEG of 2.8–52.5 GJ·ha−1 and an EROEI of 1.2–1.7 for maize ethanol production systems, as well as a NEG of 59.3–188.7 GJ·ha−1 and an EROEI of 2.2–10.2 for maize biogas production systems. Bioenergy produced in low-intensity eco-agricultural systems could therefore be an important source of energy with immense net benefits for local and regional end-users, provided a more efficient use of the co-products is ensured.