Edible insects offer an efficient source of alternative protein, requiring less land, water and emitting less greenhouse gas than conventional livestock. However, their successful integration into the food supply chain demands reliable species authentication to control allergen exposure, prevent adulteration, and meet regulatory standards. Near-infrared spectroscopy provides a rapid analytical tool, but its performance drops when applied to production batches unseen during training due to batch-to-batch variation in spectral measurements. We introduce the Batch-Invariant Spectral Network (BISN), an end-to-end framework that combines a learnable preprocessing module, initialised with Savitzky-Golay filtering, with an entropy-regularised adversarial objective to suppress batch-specific spectral variation. In contrast to Domain-Adversarial Neural Networks, which enforce domain adaptation only after feature extraction, BISN suppress batch-effects before species-specific features are learned. Using 2,700 spectra from three species (Acheta domesticus, Hermetia illucens, and Tenebrio molitor) collected across three independent production batches, BISN achieves a mean leave-one-batch-out accuracy of 0.93 (standard deviation 0.04), outperforming the strongest baseline by four percent. Further insights gained by using explainable AI confirm that model decisions consistently rely on the lipid and protein absorption regions across all folds, connecting predictive performance to known insect biochemistry. BISN addresses both cross-batch robustness and biochemical interpretability for automated insect species authentication under realistic industrial conditions. The source code and dataset are publicly available at https://github.com/majharB/bisn.

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