The impact of the milling process on the microbiological quality of yam flour produced from dried yam chips was investigated. Dried yam chips samples were procured from markets in Lagos, Ogun and Oyo states, southwestern Nigeria. Total viable bacterial count for Dioscorea rotundata (white yam) flour milled across the three locations range from 2.5x105 to 4.33x105 cfu g-1 while D. alata (water yam) flour ranged from 2.03x105 to 4.72x105 cfu g-1. Yam chips milled in the market had significantly higher (p<0.05) total viable bacterial count compared to those milled in the laboratory. Milling machines at Ibadan market harboured the significantly highest microbial count (2.1x103 cfu cm-1). All the yam flour samples milled in the market had Bacillus megaterium and Staphylococcus saprophyticus. Fusarium oxysporum, Aspergillus niger and Rhizopus nigricans were isolated from both white yam flour and water yam flour. Milling introduced some fungi known to produce mycotoxins into the yam flour. Milling yam chips into flour in the machines available at the markets increased the microbiological contamination of the yam chips by between 101->102 folds due to some unhygienic practices observed during the milling and this has implications for the microbiological quality and safety of the yam flour meal consumed. Educating processors of yam flour on the importance of regular cleaning of milling machines and avoiding collection of flour spilled on the floor into the lot to be consumed will assist in ensuring that best practices are complied with and consumers have access to safer yam flour.