Bats are potentially exposed to pesticides via foraging in croplands. Common pesticides like organophosphates are neurotoxic for vertebrates and even low doses can impair essential processes such as locomotion and cognition. These sublethal effects are usually studied using molecular biomarkers with limited ecological relevance. Behavioral studies, in contrast, represent a more informative yet sensitive approach. Spatial navigation, for example, is an ecologically relevant behavior that is modulated by cellular pathways potentially targeted by neurotoxicants. We evaluated whether bats’ ability to memorize and navigate novel spaces was negatively affected by environmental relevant doses of chlorpyrifos, a common organophosphate insecticide. We also tested how the behavioral response correlated with molecular biomarkers. We orally dosed captive big brown bats (Eptesicus fuscus) with chlorpyrifos and studied exploratory behavior in two testing arenas. We evaluated similarity of stereotype flight trajectories in a flight tent, and associative memory in a Y-maze. We quantified brain cholinesterase (ChE) activity as a cellular biomarker and employed non-targeted proteomics as molecular biomarkers. Bats exposed to chlorpyrifos were less explorative and made more incorrect choices in the Y-maze, but the consistency of their flight trajectories was unaffected. Exposed bats had 30% lower ChE activity, showed down-regulation of proteins involved in memory (VP37D), learning and sound perception (NOX3). Other important nervous system processes such as synaptic function, plasticity, oxidative stress, and apoptosis were enriched in chlorpyrifos-exposed bats. These results support the sensitivity of behavior as a biomarker of toxicity and the importance of considering other levels of organization to help explain the mechanisms underlying altered behavior due to human activities.