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The technology of green fodder production is especially important in arid and semiarid regions. Hydroponics improves on average the amount of crops in the same space, as traditional soil-based farming and can reduce water consumption compared to traditional farming methods. Limited research has been carried out on the use of hydroponic fodder and milk quality. A comparative study of traditional (Malta farm) and hydroponic fodder (Gozo farm) was conducted in Malta with 20 cows of the Holstein–Friesian breed from two farms. Individual and bulk-tank milk samples were collected once a week for a period of 1 month in order to evaluate physical (pH, conductivity, density, freezing point) and chemical (fat, protein, ash, lactose, solid nonfat) parameters as well as mineral (Zn, Cu, Pb, Ba) content. Milk proximate and physical data were processed by analysis of variance (ANOVA) for repeated measures and an ANOVA procedure with farm and time as effects for minerals. The results indicated differences in fat content and pH, showing higher values (P < 0.05) in milk samples of cows fed with the hydroponic rather than the traditional fodder; a significant time effect (P < 0.001) was found in all qualitative analyses except for lactose and salts. Minerals were in the range as reported elsewhere; Cu and Pb content was significantly higher (P < 0.001) in the Gozo farm than the one in Malta, whereas Zn content showed higher values in Malta (P < 0.001) than Gozo. Although the proximate results were similar for both farms, except for the higher fat content for the Gozo farm, principal component analysis (PCA) revealed that milk quality for the Gozo farm was superior to that of the Malta farm. However, further studies are needed to determine the effects of different hydroponic fodder using a large herd size. peer-reviewed