This work describes Langmuir–Blodgett (L–B) monolayer and multilayer assemblies constructed from a series of NLO-active azo-benzene derivatives possessing terminal moieties of variable dipole moment. The terminal groups are electron acceptors (acetyl, nitro, and cyano) and are connected to a common amphiphilic azo-benzene segment. Our experimental and theoretical results show that the interplay between two dominant non-covalent interactions within the assemblies, namely dipolar and π−π stacking interactions, dictate the packing density, structural order, as well as the electronic properties of the final films. L–B films of the acetyl derivative, which has the weakest total dipole across the azo-benzene chromophore, exhibits the highest packing density and the largest blue shift in the UV–visible absorption spectrum. This is rationalized by relatively strong π−π interactions between the azo-benzene chromophores overwhelming weak intermolecular dipole–dipole interactions. More importantly, the small internal dipole in the acetyl functional groups encourages packing in a configuration that lowers the overall energy and increases the packing density. In the case of the cyano and nitro derivatives, both L–B films show decrease in packing density and a weaker electronic coupling due to unfavorable overall dipole interaction that offsets the π−π interaction. We show that such unfavorable interactions lead to the formation of a staggered and loosely packed configuration. Our work demonstrates that a subtle difference in molecular structure can have a dramatic impact on aggregation, and consequently on the electronic and optical properties of nano-assemblies. This work demonstrates a way of controlling the formation of nanoscale structures at the molecular level through the control of noncovalent interactions.