Excitatory and inhibitory transmission onto lateral habenula (LHb) neurons is instrumental for the expression of positive and negative motivational states. However, insights into the molecular mechanisms modulating synaptic transmission and the repercussions for neuronal activity within the LHb remain elusive. Here, we report that, in mice, activation of group I metabotropic glutamate receptors triggers long-term depression at excitatory (eLTD) and inhibitory (iLTD) synapses in the LHb. mGluR-eLTD and iLTD rely on mGluR1 and PKC signaling. However, mGluR-dependent adaptations of excitatory and inhibitory synaptic transmission differ in their expression mechanisms. mGluR-eLTD occurs via an endocannabinoid receptor-dependent decrease in glutamate release. Conversely, mGluR-iLTD occurs postsynaptically through PKC-dependent reduction of β2-containing GABAA-R function. Finally, mGluR-dependent plasticity of excitation or inhibition decides the direction of neuronal firing, providing a synaptic mechanism to bidirectionally control LHb output. We propose mGluR-LTD as a cellular substrate that underlies LHb-dependent encoding of opposing motivational states.