Camel milk value chain experiences a lot of constrains which are likely to leads to high post-harvest losses due to physicochemical and microbiological changes. However, the magnitude of these quality and quantity losses have not been quantified. The objective of this study was to quantify these losses at different stages along the camel milk value chain. The study established the mean pH along the Isiolo value chain to range from 6.5 to 6.6 and did not show significant (p>0.05) difference along the chain. The percentage lactic acid ranged from 1.63 to 2.07 and showed significant (p<0.05) different along the chain. 3.57% and 4.76% of milk at delivered at bulking/cooling hub in Isiolo town and terminal market at Eastleighin Nairobi,respectively, failed alcohol test. Total viable count (TVC) showed the highest count along the chain (1.78x106 to 8.1x108) while Staphylococcus aureus showed the lowest count along the chain (1.3x104 to 2.0x106). Generally the microbial counts increased along the chain. This could be due to the longer withholding time of the milk at the various points along the chain. More milk was lost due to Total viable count standard than coliform counts standard, 100% of milk at the terminal Eastleigh market, Nairobi were rejected due to TVC while 92.5% rejected due to coliform counts. Camel milk value chain was therefore shown to be of poor microbiological quality which results to a lot of milk post-harvest losses.