Toxic pyrrolizidine alkaloids (PAs) and their N-oxides (PANOs) can be present in bee pollen depending on the plants visited by bees. A liquid chromatography-mass spectrometry (LC-MS/MS) method was developed and validated to monitor 17 PAs/PANOs in 44 bee pollens. The CIE-L∗a∗b∗ colour coordinates with the specular component either included or excluded were recorded in pellets and ground aliquots. Lightness (L∗) and yellowness (b∗) of ground bee pollen were significantly correlated to PAs/PANOs content. The L∗ and b∗ cut-offs sorted by a receiver operating characteristic analysis to predict PAs/PANOs presence showed a significant increase in the relative risk to detect amounts higher than 84 μg kg−1. Two supervised canonical discriminant analyses confirmed that pollen without PAs could be distinguished from those containing PAs/PANOs. The data suggest that instrumental colour coupled with supervised models could be used as a screening test for PAs/PANOs in bee pollen, before the confirmatory LC-MS/MS analysis.