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Abstract Novel organic heterostructures fabricated with a bilayer consisting of an axially substituted silicon phthalocyanine (R2‐SiPc) derivative and lutetium bis‐phthalocyanine (LuPc2) are investigated for their ammonia sensing properties. Surface and microstructure characterization of the heterostructure films reveal either compact or highly porous surface topography in (345F)2‐SiPc and Cl2‐SiPc‐based heterostructures, while electrical characterization reveals a strong influence of the axial substituent in R2‐SiPc on NH3 sensing capabilities. Electrical characterization further demonstrates an apparent energy barrier for interfacial charge transport, which is higher in the (345F)2‐SiPc/LuPc2 heterojunction device. In‐depth charge transport studies by impedance spectroscopy further reveal a resistive interface in (345F)2‐SiPc/LuPc2 and faster bulk and interfacial charge transport in Cl2‐SiPc/LuPc2 heterojunction devices. Different interfacial charge transport capabilities and surface topographies affect NH3 sensing properties of the two heterojunction devices, in which (345F)2‐SiPc/LuPc2 reveals a fast and non‐linear response with a limit of detection (LOD) of 310 ppb, while Cl2‐SiPc/LuPc2 exhibits a slow, and linear response to NH3 with LOD of 100 ppb. Finally, different metrological parameters of the two sensors are correlated to the respective gas‐material interactions, in which adsorption and diffusion regimes are modulated by the surface topography and hydrophobicity of the sensing layer.