The use of both naturally occurring and synthetic pigmented wood has been prevalent in woodcraft for centuries. Modern manifestations generally involve either woodworkers’ aniline dyes, or pigments derived from a special class of fungi known as spalting fungi. While fungal pigments are more renewable than anilines and pose less of an environmental risk, the carrier required for these pigments—dichloromethane (DCM)—is both problematic for humans and tends to only deposit the pigments on the surface of wood instead of evenly within the material. Internal coloration of wood is key to adoption of a pigmenting system by woodworkers. To address this issue, five solvents that had moderate solubility with the pigments extracted from Chlorociboria aeruginosa and Scytalidium cuboideum were identified, in the hopes that a reduction in solubility would result in a greater amount of the pigment deposited inside the wood. Of the tested solvents, acetonitrile was found to produce the highest internal color in ash, Douglas-fir, madrone, mountain hemlock, Port-Orford cedar, Pacific silver fir, red alder and sugar maple. While these carrier solvents are not ideal for extracting the pigments from the fungi, acetonitrile in particular does appear to allow for more pigment to be deposited within wood. The use of acetonitrile over DCM offers new opportunities for possible industrial spalting applications, in which larger pieces of wood could be uniformly pigmented and sold to the end user in larger quantities than are currently available with spalted wood.