New glutamic acid (Glu) and polyethylenimine (PE) functionalized ultra-stable gold nanoparticles (PE-Glu-AuNPs) were developed via a simple NaBH4 reduction method. The low toxicity and biocompatibility of PE-Glu-AuNPs were confirmed via an MTT assay in Raw 264.7 cells. Excitingly, PE-Glu-AuNPs were found to be extremely stable at room temperature up to six months and were utilized in an effective colorimetric naked eye assay of clenbuterol (CLB) and ractopamine (RCT) at pH 5. It was found that the selective assay of CLB and RCT is not affected by any other interferences (such as alanine, phenylalanine, NaCl, CaCl2, threonine, cysteine, glycine, glucose, urea and salbutamol). Furthermore, the detection of these β-agonists can be visually accomplished through change color from wine red to purple blue. Notably, the aggregation induced detection of CLB and RCT was well confirmed through transmission electron microscopy (TEM) and dynamic light scattering (DLS) studies. DLS investigations, clearly showed, that in the presence of CLB and RCT, the initial size of PE-Glu-AuNPs (12.8 ± 8.6 nm) was changed to 84.8 ± 52.3 and 79.5 ± 47.8 nm, respectively, via aggregation. Furthermore, the colorimetric assays of CLB and RCT with PE-Glu-AuNPs were effective starting from CLB and RCT concentrations of 200 nM and 400 nM, respectively, and could be visualized using the naked eyes. Remarkably, UV-vis titrations of PE-Glu-AuNPs with CLB and RCT could be used to well estimate their sub nanomolar detection limits (LODs) via standard deviation and linear fittings. The contribution of surface functional groups that support the analyte recognition was confirmed by fourier-transform infrared spectroscopy (FTIR) analysis. Moreover, the CLB and RCT assays with PE-Glu-AuNPs were supported by examination of human urine samples.