Behavioural states like anxiety, preference selection, and social interaction promote homeostasis and survival by facilitating effective adaptation and communication. The interstitial nucleus of posterior limb of anterior commissure, lateral (IPACL) has been suggested to play a role in regulating locomotion activation, avoidance behaviours, energy balance and processing of reward and aversive memories. However, how IPACL neurons are concurrently involved in these diverse functions remain unclear. To tackle these questions, we use deep brain Ca2+ imaging in the IPACL with miniature microscopes in freely moving mice across various behavioural contexts, including innate fear, anxiety, place preference, and social interaction. Here, we show that IPACL neurons play a role in encoding various behavioural states, with a majority showing higher responsiveness to negative stimuli. Longitudinal imaging reveals neuronal flexibility in switching encoding states based on context, with stronger imprinting observed in neurons encoding negative valence. Ensembles encoding responses to aversive stimuli, for instance, show greater specificity in their activity than those encoding safety and social responses. Our findings from optogenetic inhibition of activity-labelled ensembles provide additional evidence suggesting that ensembles exhibit flexibility in behaviour encoding and they serve as reserves in assistant of behavioural integration.This flexibility is potentially influenced by varies of circuit inputs from other brain regions. Finally, through single-cell sequencing, we confirm this functional flexibility by identifying overlaps in gene expression within activity-labelled ensembles. This comprehensive characterisation of the molecular basis of behavioural integration in the IPACL sheds light on its potential implications in both health and disease.