Fruit tree orchards are an important land-use type in the Mediterranean regions despite limited information on their potential role as carbon sinks to mitigate climate change and their capacity to store soil organic carbon (SOC). The objective of this study was to evaluate the ability of peach orchards (Prunus persica (L.) Batsch) to fix and accumulate carbon (C) in three contrasting management systems. The first system was representative of the current management recommended to French producers with high yield objectives (REF). The second system was managed with a Low-Input strategy (LI-1) for chemical pesticide application (−70%), nitrogen fertilization and water irrigation (~−25%). Lastly, the third system (LI-2) had the same low-input strategy but included a higher planting density (~2-fold) and a new tree shape training system. The experiment was conducted in the South of France for 7 years from planting (2013–2019). The aboveground biomass and C repartitions in various components of systems (tree organs and grass growing in alleys) were carried out by destructive measurements each year to determine Net Primary Production (NPP), Net Ecosystem Production (NEP) and Net Ecosystem Carbon Balance (NECB).The REF system had very high productivity during the mature tree period with 45.9 Mg ha-1 yr-1 of fresh fruit yield and 16.8 Mg ha-1 yr-1 of aboveground biomass, corresponding to 7379 kg C ha-1 yr-1 (738 g C m-2 yr-1). Orchard NPP (tree and grass) reached 11,003 ± 353 kg C ha-1 yr-1 (1100 ± 35 g C m-2 yr-1) and soil respiration was 3366 ± 776 kg C ha-1 yr-1 (337 ± 78 g C m-2 yr-1) leading to an NEP of 7637 ± 853 kg C ha-1 yr-1 (764 ± 85 g C m-2 yr-1) and an NECB of 4919 ± 858 kg C ha-1 yr-1 (492 ± 86 g C m-2 yr-1). Carbon accumulation was distributed 53% in perennial biomass, and the soil had an annual SOC stock change of 3.8‰. In the LI-system, the reduction of inputs and chemical pesticides did not impact the average NEP and NECB, even though pest infestations reduced biomass in 2015 and 2019. The same input reductions in the LI-2 system but with increased planting density provided significant increases in NPP (+10.5%) and NEP (+20.0%), leading to an NECB of 5876 ± 890 kg C ha-1 yr-1 (588 ± 89 g C m-2 yr-1), or 19.4% greater than the REF system during the mature tree period. This positive C accumulation was distributed 46% in the perennial biomass, which could reach 35.5 Mg C ha-1 (3550 g C m-2) after 15 years of orchard life. The SOC stock change was 10.0‰ in the LI-2 system, greater than the 4‰ initiative of the Paris COP21. Innovative peach orchards with agroecological management can mitigate environmental impacts by combining high-quality fruit production with enhanced CO2 sink capacity objectives.