We report on the structure and morphology of 5,5′-bis(naphth-2-yl)-2,2′-bithiophene (NaT2) films in bottom-contact organic field-effect transistors (OFETs) with octadecyltrichlorosilane (OTS) coated SiO2 gate dielectric, characterized by atomic force microscopy (AFM), grazing-incidence X-ray diffraction (GIXRD), and electrical transport measurements. Three types of devices were investigated with the NaT2 thin-film deposited either on (1) pristine SiO2 (corresponding to higher surface energy, 47 mJ/m2) or on OTS deposited on SiO2 under (2) anhydrous or (3) humid conditions (corresponding to lower surface energies, 20–25 mJ/m2). NaT2 films grown on pristine SiO2 form nearly featureless three-dimensional islands. NaT2 films grown on OTS/SiO2 deposited under anhydrous conditions form staggered pyramid islands where the interlayer spacing corresponds to the size of the NaT2 unit cell. At the same time, the grain size measured by AFM increases from hundreds of nanometers to micrometers and the crystal size measured by GIXRD from 30 nm to more than 100 nm. NaT2 on OTS/SiO2 deposited under humid conditions also promotes staggered pyramids but with smaller crystals 30–80 nm. The NaT2 unit cell parameters in OFETs differ 1–2% from those in bulk. Carrier mobilities tend to be higher for NaT2 layers on SiO2 (2–3 × 10–4 cm2/(V s)) compared to NaT2 on OTS (2 × 10–5–1 × 10–4 cm2/(V s)). An applied voltage does not influence the unit cell parameters when probed by GIXRD in operando.