Accurate representation and localization of relevant objects is important for robots to perform tasks. Building a generic representation that can be used across different environments and tasks is not easy, as the relevant objects vary depending on the environment and the task. Furthermore, another challenge arises in agro-food environments due to their complexity, and high levels of clutter and occlusions. In this paper, we present a method to build generic representations in highly occluded agro-food environments using multi-view perception and 3D multi-object tracking. Our representation is built upon a detection algorithm that generates a partial point cloud for each detected object. The detected objects are then passed to a 3D multi-object tracking algorithm that creates and updates the representation over time. The whole process is performed at a rate of 10 Hz. We evaluated the accuracy of the representation on a real-world agro-food environment, where it was able to successfully represent and locate tomatoes in tomato plants despite a high level of occlusion. We were able to estimate the total count of tomatoes with a maximum error of 5.08% and to track tomatoes with a tracking accuracy up to 71.47%. Additionally, we showed that an evaluation using tracking metrics gives more insight in the errors in localizing and representing the fruits.