Open-air markets are a popular market channel for most agri-food products in developing countries. In the peri-urban areas of Kenya, these are the most convenient sources of fresh fruits and vegetables for many households. However, the haphazard organization and management of these markets often results in insecurity and other economic losses. Yet, no empirical study has delved in the analysis of the extent of these challenges and remedial measures. In order to address this critical policy issue and advance knowledge in this area, the present study analyzed peri-urban food traders’ preferences for the design and management attributes of open-air markets in Nairobi, Kenya. A total of 120 agri-food traders were randomly selected and interviewed from open-air markets. The results of a choice experiment survey showed that traders prefer the management of these markets through clearly structured county government procedures, allocation of market space on monthly rotational basis and restriction of space to each user. Further, the study observed that traders prefer comprehensive services provision based on competitive tendering processes. These findings call for reforms in the management and design of open-air markets in order to improve service delivery and security of all participants.