Due to a continuous abandonment of marginal agricultural land, Mediterranean pine forests are growing both in biomass stock and area but remain mainly unmanaged. Pinus halepensis is one of the main pioneer species with strong expansion throughout the Mediterranean basin. In mature forests and pole stands, selective thinnings aimed to eliminate dominated and dead trees are necessary to improve the resilience and persistence of these forest ecosystems. Bioenergy market provides an opportunity to mobilise this woody material, helping to prevent and reduce wildfires in a context of climate change and energy transition. Despite the existing expertise on wood harvesting, there is a lack of practical knowledge about cost-effective methods for bioenergy use of selective thinnings in such forests. The objective of this study was to compare thinning harvesting methods in representative 63-year-old Pinus halepensis afforestation in pole stage for bioenergy uses, following the silvicultural treatments defined in the Spanish forest management plan. Time studies were performed over six representative plots in Navalón (Spain). Treatments included three plots with the traditional stem wood method combined with the logging of forest residues (integrated system), and three plots with the whole tree chipping (whole tree system). Time, productivity and fuel consumption were recorded for both systems. A woodchip quality assessment of each assortment was performed in the laboratory according to European standards. The results obtained demonstrated that time consumption and productivity were similar between the integrated harvesting system and the whole tree system. Regarding the total energy balance, it should be noted that both systems produce woodchips that contain over ten times more energy than that required to mobilise and process the obtained biomass. Fuel consumption, costs and degree of damage were slightly higher in the whole tree system due to the more intensive forwarding operation. The two assortments of woodchips in the integrated system had a higher (chipped log material) and lower quality (chipped crown material) than whole tree woodchips. In conclusion, integrated harvesting is a better option to diminish fuel consumption, cost and environmental impact, and also to obtain better quality woodchips for the production of added value biofuels (pellets).