Dairy plays an important role in the diet of Borana pastoral communities of Ethiopia, but poor hygiene during milk production, handling and processing coupled with raw milk consumption are significant health risks for consumers. We conducted experiments to assess the effect of different practices on bacterial quality of traditional yogurt. In a field trial, we investigated the impact of using stainless-steel containers instead of traditional containers made of interwoven fibers on bacterial load and the cultural acceptability of the steel container for yogurt preparation. In a laboratory experiment, we assessed the effect of sanitizing milk containers with smoke from 3 tree species (Olea europaea ssp. africana, Faurea speciosa and Terminalia brownii), 2 milk containers (traditional vs. stainless steel) and 2 smoking methods (introducing the burning wood in the container vs. fumigation) on bacterial loads. The field trial showed that the bacterial loads of the yogurt prepared using traditional and stainless-steel milk containers did not differ (P < 0.05). Most of the informants appreciated the stainless-steel container because it could be easily sealed with a lid. However, they reported no desire to use it as substitute to the traditional container because (1) it becomes hot during the day and cold during the night, which accelerates souring of milk and (2) it does not have the traditional decorations. Moreover, 55.8% of the respondents indicated that yoghourt prepared using the traditional container had a better taste. The lab experiment showed that the traditional container (P < 0.001) and smoking by putting the burning wood inside the container (P = 0.013) reduced bacteria loads compared with the alternatives. Similarly, Olea tree species was more effective than others at reducing bacterial loads. Our results suggest that the use of stainless steel containers did not add value for the Borana pastoral communities as it did not reduce bacterial load of yogurt and the container acceptability among end-users was low.