The fruit quality parameters of Prunus armeniaca L. cv ‘Ninfa’ grafted on ‘Myrobalan 29C’ (Prunus cerasifera Ehrh.) and ‘Real Fino’ apricot seedling (Prunus armeniaca L.) were analysed in an experimental orchard under organic management. The study was performed between 2010 and 2012 in the province of Seville (SW Spain). Colour, fruit and stone weights, firmness, soluble solid concentration, and acidity were measured for fruit quality evaluation. Trunk cross-sectional area, main branches, and fruit yield were also determined. In general, ‘Myrobalan 29C’ rootstock produced fruit slightly larger in size and with a bigger weight. By contrast, apricots on ‘Myrobalan 29C’ had less firmness and a lower solid soluble concentration than on ‘Real Fino’. There was little difference in the colour, acidity, and stone dry weights. Trees on ‘Real Fino’ had larger areas of trunk and branches but no significant differences were obtained in relation to fruit yields.