Carbon sequestration and storage in biomass is one of the most important measures to mitigate climate change. Mediterranean woody crops can sequestrate carbon in the biomass of their permanent structures for decades; however, very few studies have focused on an assessment of biomass and carbon sequestration in these types of crops. This study is the first to estimate above- and belowground biomass carbon stock in Mediterranean woody crops through a bottom-up approach in the NE Iberian Peninsula in 2013. Moreover, this is the first time that an assessment of the annual changes in carbon stock in the study area over a six-year period is presented. For this purpose, eight crop- and site-specific equations relating biomass or biometric variables to crop age were calculated. Most of the data were our own measurements, but unpublished data supplied from other authors as well as data from literature were also considered. Census of Agriculture data was used to scale results from individual data up to the municipality level at the regional scale. Results show that in woody cropland in NE Spain the total biomass carbon stock in 2013 was 5.48 Tg C, with an average value of 16.44 ± 0.18 Mg C ha−1. Between 2013 and 2019, although there was a 2.8% mean annual decrease in the area covered by woody crops, the carbon stock in the biomass of these crops increased annually by 3.8% due to the growth of the remaining woody cropland. This new estimation of carbon stocks may contribute to better understand carbon balances and serve as a baseline to global inventories. It may also serve to assess and manage carbon storage as an ecosystem service provided by Mediterranean woody cropland for mitigating climate change and, in combination with adaptive strategies, for supporting a productive and resilient agro-food system.