The advent of cluster ion beams has paved the way to the routine 3D analysis of organic heterojunctions. Alternatively, organic thin layers have also been successfully depth profiled with a low-energy cesium ion beam (Cs+), to exploit the high chemical reactivity of cesium atoms, acting as free-radical scavengers. Despite of this, little is known about the depth resolution associated with low-energy Cs+ sputtering on organic multilayers. In this work, amino acids multilayers, consisting of phenylalanine delta layers alternated with tyrosine spacers, were used as model systems to assess the depth resolution associated with 500 eV Cs+ depth profiles. High yields were obtained for quasi-molecular ions from both amino acids, and no significant chemical alteration was noticed under the monoatomic bombardment. A depth resolution as low as 4 nm is demonstrated without sensible degradation on a rather long profile depth (300 nm). Limited depth resolution (> 10 nm) along with high molecular degradation was previously reported on similar systems by combining low-energy Cs+ with Ga+ analysis beam. The use of the Bi3+ analysis beam results in a dramatic improvement of both the characteristic molecular signal intensities and the depth resolution. Even though the analysis beam fluence is very low compared to the sputtering beam fluence, data suggest that further reducing the analysis Bi3+ fluence could improve the depth resolution by ~ 1 nm.