Restoration programs improve the quality of degraded ecosystem and play a role in mitigating climate change. Selection of plant species based on carbon sinks has been widely used in such programs, including using fruit trees. The purpose of this study was to estimate the carbon stock of several local fruit species collections at Purwodadi Botanic Garden in order to determine their potential as carbon storage. Above ground C stock estimation was conducted using a non-destructive method by measuring stem diameter at breast height (DBH) and tree height. The age of sampled fruit trees ranged between 20–60 years. Biomass was obtained by calculating using allometric equation. The results showed that sixty years old Diospyros malabarica (Desr.) Kostel. stored the highest carbon (163 Mg C.ha−1). Whereas, the lowest carbon stock was stored by forty years old Stelechocarpus burahol (Blume) Hook.f. & Thomson (1.4 C tonnes.ha−1). Findings of this study suggested that most observed local fruit trees are potential carbon sinks and must be promoted in restoration programs to help mitigate climate change. Diospyros malabarica (Desr.) Kostel, Flacourtia rukam Zoll. & Moritzi, Garcinia dulcis (Roxb.) Kurz,, Protium javanicum Burm.f, Sandoricum koetjape (Burm.f.) Merr., and Syzygium cumini (L.) Skeels were recommended as priority species for restoration.