High-throughput platforms for plant phenotyping usually demand expensive high-density LiDAR devices with computational intense methods for characterizing several morphological variables. In fact, most platforms require offline processing to achieve a comprehensive plant architecture model. In this paper, we propose a low-cost plant phenotyping system based on the sensory fusion of low-density LiDAR data with multispectral imagery. Our contribution is twofold: (i) an integrated phenotyping platform with embedded processing methods capable of providing real-time morphological data, and (ii) a multi-sensor fusion algorithm that precisely match the 3D LiDAR point-cloud data with the corresponding multispectral information, aiming for the consolidation of four-dimensional plant models. We conducted extensive experimental tests over two plants with different morphological structures, demonstrating the potential of the proposed solution for enabling real-time plant architecture modeling in the field, based on low-density LiDARs.