The growing intensity and frequency of fires and volcanic activity have heightened the demand for real-time monitoring of thermal events. This Thesis presents the first comprehensive end-to-end processing pipeline for real-time segmentation of thermal hotspots in raw multispectral imagery. The pipeline combines an onboard Deep Learning (DL) design with the use of raw imagery to achieve real-time performance. The processing pipeline was thoroughly tested on CubeSat edge computing hardware, demonstrating its feasibility for CubeSats with limited computing resources. The DL architecture used was specifically designed in this project to address onboard constraints such as model size, complexity and inference time. The satellite imagery used in this work is from the Sentinel-2 mission, and a key contribution of this project is the creation of SegTHRawS, the first dataset for thermal hotspot segmentation in raw multispectral imagery.