This study quantifies the synergies between agriculture and bioenergy considering biodiesel production as part of a set of systemic initiatives. We present a case study in Ecuador taking into account the recent government measures aimed at developing the bioenergy sector. Four scenarios have been evaluated through a newly designed systemic scheme of circular-economy initiatives. These scenarios encompass three production pathways covering three energy crops: palm oil (PO), microalgae in open ponds (M1) and microalgae in laminar photobioreactors (M2). We have applied Benefit-Cost Analysis (BCA) methodology considering the Net Present Value (NPV) and the Benefit-Cost Ratio (BCR) as the main evaluation criteria. In terms of private investment, biodiesel production from PO is more attractive than from M2. However, regarding efficiency and effectiveness of public funds, M2 is superior to PO because the public BCR and NPV are higher, and the pressure on agricultural land is lower. Moreover, M2 as part of a systemic approach presents a better carbon balance. These findings show that, under a systemic approach based on circular economy, strategies like the one analyzed in this study are economically feasible and may have a promising future.