Opioids are powerful analgesics but carry many contingencies that can lead to opioid-use disorder. Significant energy has been invested in understanding the molecular actions of the opioid alkaloids, particularly their relationship with the opioid receptors at the cell surface. However, there is growing awareness of the opioid-receptor-independent and intracellular actions of opioids that may contribute to their overall pharmacology. The investigation of these interactions is stymied by a lack of relevant opioid chemical tools to probe intracellular actions of the opioids. To investigate the intracellular interactions of the opioids, we designed and developed two opioid probes: photo-click morphine (PCM-2) as a photo-affinity probe for morphine and dialkynyl-acetyl morphine (DAAM) as a metabolic acetate reporter for heroin. Application of these probes to SH-SY5Y, HEK293T, and U2OS cells revealed that PCM-2 and DAAM primarily localize to the lysosome by confocal microscopy and chemical proteomics studies. Interaction site identification by mass spectrometry revealed the mitochondria phosphate carrier protein, solute carrier family 25 member 3, SLC25A3, and histone H2B as acetylation targets of DAAM. This study provides the first chemical probes for the study of the intracellular targets of opioid alkaloids.