We report on the apparent structure of 5,5″-bis(naphth-2-yl)-2,2′:5′,2″-terthiophene (NaT3) in organic field-effect transistors (OFETs) with and without embedded silver nanoparticles. Using regular- and microbeam grazing incidence wide- and small-angle X-ray scattering, the device structure is characterized locally in the area with the embedded particles. The NaT3 thin film order is reduced and the found unit cell (a = 25.7 Å, b = 5.87 Å, c = 8.03 Å, and β = 98.9°) differs significantly from the one reported in the bulk, but shows no significant change, when the particles corresponding to the crystal size are incorporated into the device structure. At the same time, the apparent thin film crystal sizes in OFETs are found to be similar with and without the embedded particles. In both cases, the carrier mobilities are of the order of 10−4 cm2/(V s).