To gain better control over the characteristics of the alkanethiol-capped silver nanoparticles (SNP) prepared by the two-phase method, the intermediate stage of this reaction and the structure of the precursor compound were investigated. Samples taken from the intermediate stage of the reaction were analyzed by NMR and vibrational spectroscopy both in solution and after solvent removal. The H-1 NMR chemical shifts of the complexes formed during the phase-transfer step were used to detect any structural changes that occur upon introduction of nonanethiol. Moreover, the presence of silver thiolate was monitored by comparing the FTIR and Raman spectra of silver nonanethiolate with the dried samples. Further insights into the microstructure of the intermediate compounds were sought by characterizing samples differing in molar ratios of tetraoctylammonium bromide (TOAB) to silver nitrate (AgNO3). C-13 solid-state NMR chemical shifts, C-13 relaxation times, and the DSC transitions of these samples revealed a dependence of their phase structure on the initial concentration of the reagents. At least two phases with distinct mobility and conformational ordering of their octyl chains were identified in the samples prepared with excess TOAB, which was associated with the presence of multiple anionic species. The observations regarding the composition of the phase-transfer product were further related to the quality of the resulting nanoparticles. It was demonstrated that a large excess of TOAB, which is commonly used in two-phase methods, can be avoided without compromising the size and dispersity of the silver nanoparticles produced. This modification to the synthetic procedure simplifies the purification of the product, mitigates the propensity of the nanoparticles for aggregation, and facilitates their redispersion.