Ca3Co4O9 and Ca2.8Bi0.2Co4O9 thin films were fabricated on LaAlO3 (LAO) substrate using pulsed laser deposition technique and were studied for their thermoelectric (TE) properties in Stranski–Krastanov mode for the first time. The thin films consisted of 3D clusters/islands on a ∼14-nm thick 2D layer with cluster density being higher for Ca2.8Bi0.2Co4O9 thin films. The clusters also represent areas of dislocation and therefore act as carrier scattering centers, which leads to a temperature-activated type conductivity. Seebeck coefficient as high as 136 and 163 μ V/K was measured for the Ca3Co4O9 and Ca2.8Bi0.2Co4O9 thin films, respectively, which is among the highest reported values for this system. The 3D island formation was also found to be useful in reducing the thermal conductivity of the thin film/substrate system by increased phonon scattering. This work shows that the island formation in thin films can be utilized as a means of enhancing TE properties of a thin film system, however, a detailed work including optimization of the film thickness and cluster/inland density is required.