Polyelectrolyte templating effectively suppresses the aggregation of cationic hemicyanine-based amphiphiles in monolayer Langmuir-Blodgett (LB) films leading to enhanced and stable optical second harmonic generation (SHG). The current study explores the impact of different polyelectrolytes (salts of poly(4-styrenesulfonic acid), deoxyribonucleic acid, and carboxymethylcellulose) on the mode of formation of multilayer LB films of the hemicyanine amphiphile and their SHG response. Pressure-area isotherms and Brewster angle microscopy reveal the impact of the polyelectrolyte complexation on the Langmuir films. Transfer ratios observed during film deposition, supported by electronic absorption spectra and atomic force microscope images of the multilayer LB films, suggest that the polyanions influence the deposition sequence, leading to significant variations in the SHG. Carboxymethylcellulose is identified as an optimal template that induces favorable z-type deposition, leading to the formation of stable multilayer films. These films exhibit the expected quadratic increase of SHG with the extent of deposition; significantly the film response is very stable under extended laser irradiation. It is proposed that structural adjustments of the sandwiched polymer layer lead to the observed deposition sequence and film stability. Polyelectrolyte templating is demonstrated to be a simple and effective strategy for the fabrication of multilayer LB films to elicit efficient quadratic nonlinear optical response.