This study addresses the critical need for effective data fusion strategies in pest prediction for pitahaya (dragon fruit) cultivation in the Ecuadorian Amazon, where heterogeneous data sources—such as environmental sensors and chlorophyll measurements—offer complementary but fragmented insights. Current agricultural monitoring systems often fail to integrate these data streams, limiting early pest detection accuracy. To overcome this, we compared early and late fusion approaches using comprehensive experiments. Multidimensionality is a central challenge: the datasets span temporal (hourly sensor readings), spatial (plot-level chlorophyll samples), and spectral (chlorophyll reflectance) dimensions. We applied dimensionality reduction techniques—PCA, KPCA (linear, polynomial, RBF), t-SNE, and UMAP—to preserve relevant structure and enhance interpretability. Evaluation metrics included the proportion of information retained (score) and cluster separability (silhouette score). Our results demonstrate that early fusion yields superior integrated representations, with PCA and KPCA-linear achieving the highest scores (0.96 vs. 0.94), and KPCA-poly achieving the best cluster definition (silhouette: 0.32 vs. 0.31). Statistical validation using the Friedman test (χ2 = 12.00, p = 0.02) and Nemenyi post hoc comparisons (p < 0.05) confirmed significant performance differences. KPCA-RBF performed poorly (score: 0.83; silhouette: 0.05), and although t-SNE and UMAP offered visual insights, they underperformed in clustering (silhouette < 0.12). These findings make three key contributions. First, early fusion better captures cross-domain interactions before dimensionality reduction, improving prediction robustness. Second, KPCA-poly offers an effective non-linear mapping suitable for tropical agroecosystem complexity. Third, our framework, when deployed in Joya de los Sachas, improved pest prediction accuracy by 12.60% over manual inspection, leading to more targeted pesticide use. This contributes to precision agriculture by providing low-cost, scalable strategies for smallholder farmers. Future work will explore hybrid fusion pipelines and sensor-agnostic models to extend generalizability.