In order to study the consequences of the conversion from conventional to organic farming procedures from 2000 to 2011, 11,543 milk samples from a Castellana sheep farm and two Churra farms have been analysed, from 2,748 lactations (Castellana, n=1,257; Churra, n=1,491),. Milk production was higher during the conventional period compared with the organic one (385.6 ± 3.50 vs. 360.3 ± 2.80 g, respectively; P <0.001) with a higher fat content (7.2 ± 0.01 vs. 6.8 ± 0.10%; P <0.001), similar protein content (5.8 ± 0.10 vs. 5.8 ± 0.01%; P <0.10) and higher total solid content (18.4 ± 0.10 vs. 18.3 ± 0.01; P <0.001). The conversion to organic farming resulted in a reduction in somatic cell count (SCC) compared with the values obtained during the conventional period (1,039 ± 34 vs. 861 ± 23 cells x 1000 /ml; P <0.001). Prolificacy of the three flocks experienced a reduction after being transformed into an organic system (1.33 ± 0.01 vs. 1.25 ± 0.01 lambs born/lambing; P <0.0001). In conclusion, although the conversion to organic farming led to an evident reduction in milk production per lambing, a SCC decrease was observed after the conversion period. It is necessary to identify possible causes of this qualitative improvement and productive reduction, linked to the organic farming procedures as food origin, animal density, or flock management.