Canopy fuels determine the characteristics of the entire complex of forest fuels due to their constant changes triggered by the environment; therefore, the development of appropriate strategies for fire management and fire risk reduction requires an accurate description of canopy forest fuels. This paper presents a method for mapping the spatial distribution of canopy fuel loads (CFLs) in alignment with their natural variability and three-dimensional spatial distribution. The approach leverages an object-based machine learning framework with UAV multispectral data and photogrammetric point clouds. The proposed method was developed in the mixed forest of the natural protected area of “Sierra de Quila”, Jalisco, Mexico. Structural variables derived from photogrammetric point clouds, along with spectral information, were used in an object-based Random Forest model to accurately estimate CFLs, yielding R2 = 0.75, RMSE = 1.78 Mg, and an average Biasrel = 18.62%. Canopy volume was the most significant explanatory variable, achieving a mean decrease in impurity values greater than 80%, while the combination of texture and vegetation indices presented importance values close to 20%. Our modelling approach enables the accurate estimation of CFLs, accounting for the ecological context that governs their dynamics and spatial variability. The high precision achieved, at a relatively low cost, encourages constant updating of forest fuels maps to enable researchers and forest managers to streamline decision making on fuel and forest fire management.