Organic milk and dairy products are widely consumed lately, with the belief they are of higher nutritional quality than conventional, while researchers report contradictory views on this issue. This study aimed to compare the fat, protein, and lactose content of organic and conventional raw ewe’s and goat’s milk in Greece and to further associate the impact of the farming practices on these parameters. Two hundred thirty-four bulk milk samples were collected from 62 goat and 16 sheep organic and conventional farms with similar farming characteristics. A standardized detailed survey and a sampling report were used in order to record the farming practices implemented in the participating farms. The chemical composition of all samples was determined by Fourier transformed infrared analysis. Statistical associations of farming practices with the milk chemical gross composition results were explored using linear mixed-model analysis. Linear mixed-model analysis revealed several factors in farming practices such as the feeding regime, the season, and the breed to be associated with ewe’s and goat’s milk composition, while organic or conventional farm system was not identified as an associated factor. Organic and conventional goat and sheep farming in Greece does not substantially differ, and consequently, there were no significant differences found in the examined chemical composition parameters of organic and conventional goat’s and ewe’s milk.