Plants produce a wide array of pharmaceuticals in use today through a plethora of specialized metabolic pathways. Benzylisoquinoline alkaloids (BIAs) are a class of these specialized metabolites that include a diverse group of pharmacologically active compounds of great importance. BIAs can be found in a variety of plants, including the opium poppy and wide array of other plants used in traditional medicines. Amongst the most important BIAs are morphine, and its immediate biosynthetic precursor codeine. BIA biosynthetic pathways include many classes of enzymes that are capable of catalyzing many different types of rearrangements and decoration reactions. Two important classes of these enzymes are N-methyltransferases and aldo-keto reductases. To understand the molecular mechanisms at work in these two classes of enzymes, pavine N-methyltransferase and codeinone reductase were targeted for structural determinations through X-ray crystallography. Crystal structures of pavine N-methyltransferase in complex with substrates have been solved to 1.6 Å resolution. These structures reveal novel insights into substrate recognition and catalytic mechanism. Structures of apo codeinone reductase have been solved to 2.9 Å resolution and have revealed novel features regarding the quaternary structure of this enzyme. These structures reveal new details not seen in other aldo-keto reductase structures. Activity assays monitored using LC/MS, in combination with differential scanning fluorimetry, have given insight into the catalytic mechanisms behind the actions of these two enzymes.