Biomass from agricultural residue has significant potential as renewable energy resource. Therefore, cost-efficient processing and supply of agricultural residues are important to strategically plan and utilize this energy resource. This chapter describes the agricultural pruning to energy (PtE) value chains and presents the life cycle cost analysis (LCCA)-based cost assessment results, focusing on almond and peach tree pruning data obtained from Spain during 2015–2016. Along the main life cycle stages of PtE system, costs of harvesting, off-farm storage, transport, biomass loss, and management of biomass supply chain were considered. In terms of functional unit cost, the life cycle cost (LCC) was calculated to be about 126 €/t for almond PtE and 115 €/t for peach PtE value chain. In both cases, the harvesting stage was found to be cost at hot stage followed by the storage stage. The cost at harvesting stage was about 83% (of 126 €/t) and 82% (of 115 €/t) in the case of almond and peach cases, respectively. Similarly, the share of operational cost was about 74% and 76% for almond and peach cases, respectively. Therefore, more efforts should be made to improve the performance of logistics operations and management of such PtE initiatives.