Laser thin layer deposition technologies were applied to develop organic heterostructures on flexible transparent conductive electrode (TCE). Flexible substrates such as flexible glass (FG), polyethersulfone (PES), amorphous polyethylene terephthalate (PET-A) and biaxially-oriented polyethylene terephthalate (PET-B) were employed to assess the influence of the substrate type on the optical and electrical characteristics of the organic devices. For comparison reason, the organic heterostructures were fabricated on rigid glass substrate and commercially available indium tin oxide (ITO)-coated PET. Hence, flexible and rigid glass substrates were coated with ITO film by pulsed laser deposition (PLD) at low fluence, subsequently a blend layer based on zinc phthalocyanine (ZnPc) and N, N′-bis-(1-dodecyl)perylene-3,4,9,10 tetracarboxylic diimide (AMC14) being deposited by matrix assisted pulsed laser evaporation (MAPLE) on the TCE film. The investigations evidenced that the roughness and the substrate type can strongly influence the properties of the ITO layer deposited by PLD as well as the optical and electrical characteristics of the organic heterostructures based on the blend layer deposited by MAPLE. Thus, the lowest roughness (0.8 nm) and the best Hall mobility (41.9 cm2/Vˑs) were achieved for ITO coatings deposited on flexible glass substrate. Also, the highest current density value (9.3 × 10− 4 A/cm2 at 0.5 V) was reached for the organic heterostructures fabricated on this type of flexible substrate.