To clarify the effect of organic matter application on soil carbon sequestration in orchards, long-term field experiments (>10 years) were conducted at three sites (in Tsukuba, Yamanashi, and Omura) characterized by different fruit crop species, soil types, and climate. Three treatments were established in plots at all sites: (i) clean cultivation (CC, the control), in which chemical fertilizer was applied and the ground was kept bare; (ii) sod culture (SC), in which chemical fertilizer was applied and the ground was covered by grass or weeds; and (iii) organic amendment (OA), in which chemical fertilizer and cattle manure (OA_cat) or bark compost (OA_brk) were applied and the ground was kept bare. At Tsukuba, annual changes in soil organic carbon concentration (a_soc) were lowest in CC and highest in OA_cat and OA_brk plots. At Yamanashi, CC plots lost soil carbon, and a_soc increased the highest in OA_cat plots. At Omura, a_soc was negative in CC and SC plots and was positive in OA_brk plots. Within treatments, annual changes in soil organic carbon were highest in OA plots and lowest in CC plots at all sites; positive differences between control and treatment plots indicated that application of organic matter increased soil carbon sequestration.