The impact of alternative farming systems on fruit quality of orchard crops has been rarely examined. This study compared the effect of two management regimes with or without effective microorganisms (EM) on fruit quality of sweet cherry (Prunus avium L. cultivar Sweetheart). After four years, EM had no effect on quality however, fruit from regime 2 based on organic amendments and no herbicide had higher TSS and malic acid concentration but reduced size, compression firmness and stem retention force than fruit from regime 1 which was based on current conventional fertigation practices combined with herbicide application. All quality attributes reached ‘export finest’ standard for all treatments, providing evidence that organic amendment regimes can supply fruit acceptable for export markets.