This study investigated the effect of on-farm practices on milk production, chemical and microbiological quality and on Somatic Cell Count (SCC) as well as the evolution of milk quality along the camel dairy value chain in southern Tunisia. A survey of 12 periurban dairy camel farms showed that the use of machine milking is limited (16.7%). The milking hygiene practices need to be improved with only 25% of farmers practiced teat dipping and washed the material with hot water and detergents. In addition, 75% of farmers milked their animals in bedding area. Conservation and marketing conditions for raw camel milk were mediocre. Analysis of on-farm milk quality showed that use of machine milking was related to increased milk production but also caused an increase in the microbial load. Quality assessment at different stages of the production chain showed that the chemical composition of milk was conserved, whereas the physical and microbiological quality was altered. At production, the load in Mesophilic Total Aerobic Flores (MTAF) was low with 17.4 × 104 cfu/mL, compared to bulk and point of sale milk, which had a significantly higher load (21.2 × 105 cfu/mL and 61.2 × 105 cfu/mL, respectively). The acceptability threshold of Acidity, MTAF, Total Coliforms and S. aureus prevalence were exceeded in all samples purchased from points of sale. Therefore, improvements in milking hygiene, milk storage, and transport conditions are essential in order to guarantee the quality of camel’s milk to meet the needs of the consumer. Highlights The use of machine milking for dromedary camels in Southern Tunisia is limited and most she camels are milked by hand with suckling of the calf. Milking routine affect significantly the bacterial load of camel milk. Sanitation problems and keeping the cold chain are the biggest challenge in the dairy camel sector.