The road safety of vulnerable users is a current issue; in densely populated areas, the use of alternative and light mobility vehicles is growing in popularity, and their users conflict with vehicles having larger dimensions and masses. This study focuses on the risk analysis of collision between bicyclists and motorized vehicles in urban intersections. Twenty-five urban four-leg intersections, with and without bike paths, were considered in order to identify the conflict points, calculate their hazardousness, and assess the risk of collision using a probabilistic approach. Traffic light setup, yield line retraction, design of areas, and counter-clockwise circulation reserved for bicyclists are the geometrical and functional approaches proposed to mitigate the risk of collision. Two risk-based approaches proposed by the authors were implemented—the first examines all identified conflict points, while the second assesses the risk condition of the overall intersection. The obtained results show that the number of conflict points varied between 32 and 112 and the risk of collision varied between 4.57 × 10−2 and 2.46 × 10−1. The proposed assessment allowed us to make an objective comparison between the possible layouts for various traffic mixes and design conditions, and to identify the most effective solutions. Significant differences in terms of risk were found. Each mitigation strategy should be motivated by a reasoned decision considering the different needs of all road users, traffic demand, and geometrical and functional constraints.