Agricultural commodities make up a significant portion of India's freight transportation. They pass through urban areas during various supply chain stages, making urban freight essential. However, importance of urban freight often goes unnoticed, impacting efficiency, society, and the environment. In towns with agricultural hubs, issues intensify as freight vehicles block entrances and exits due to inadequate management and infrastructure. This leads to higher expenses in urban areas. The study attempts to identify certain challenges that plague the transportation of agricultural commodities in urban areas. The study is conducted in the city of Kanpur, Uttar Pradesh due to its unique character of production, processing, storage, consumption of agricultural commodities. The primary data was collected by the OD survey, establishment survey, interviews and questionnaires. The study identifies inefficiencies like empty return trips, increase in the trip lengths, along with congestion, overloading, etc. These identified issues coupled with the informality of the sector, lack of education and enforcement lead to other implications in terms of cost, emissions, and opportunity cost.