Lignin has a very complex structure, and this is partly due to the monomers being connected by many different types of covalent bonds. Furthermore, there are multiple covalent bonds between lignin and polysaccharides in wood, and it is known that the structure of lignin covalently bound to the hemicellulose xylan is different to lignin bound to the hemicellulose glucomannan. Here, synthetic lignin (DHP) is synthesized at different pH and it is shown that lignin made at lower pH has a structure more similar to the lignin bound to xylan, i.e., having higher relative content of β-O-4 ethers. It is hypothesized that xylan due to its carboxylic acids forms a locally lower pH and thus “direct” the lignin structure to have more β-O-4 ethers. The biological significance of these results is discussed.