How the brain computes decisions to support adaptive behaviours under different demands is a long-standing question. Decision-making does not solely rely on cognitive judgments but is likewise influenced by internal states. The ventral hippocampus (vH) is a higher-order cortical brain region critical for processing emotions such as anxiety. Here, we examined the influence of anxiety on decision-making processes while recording neuronal activity in the vH and medial prefrontal cortex (mPFC). We observed that the activity of vH neurons is modulated by trajectories with different anxiety levels and this effect was not a mere reflection of novelty. We additionally identified vH neurons with preferential ‘deliberating’ and ‘anxiety’ features as mice made decisions under emotional conflicts. Using selective optogenetic inhibition of vH terminals in the mPFC, we showed that mice exhibited biased decision-making selectively during trials with higher emotional conflicts. Collectively, these results suggest that vH circuits targeting mPFC mediate decision-making under emotional conflicts.