Room-temperature ionic liquids (RTILs) can be used as electrosterical stabilizers for nanoparticles without adding stabilizing agents. However, the nanoparticle stability and its mechanisms are still in discussion. We deposited preformed 2 nm ±0.6 nm silver clusters into the ionic liquid C4MIM PF6 using in situ UV/vis absorption to monitor the deposition process. The time- and temperature-dependent cluster aggregation process was studied with ex situ UV/vis absorption spectroscopy analyzed with electrodynamic calculations using generalized Mie theory. On an atomistic level, the sample structure was investigated using EXAFS and a neural network based analysis of XANES. The combination of all methods shows that an aggregation of the original 2 nm clusters without coalescence takes place, which can be controlled or stopped by choosing an appropriate sample temperature. This approach allows the controlled production of chainlike cluster aggregates in RTIL, promising for a number of applications.