Many new active pharmaceutical ingredients (API) undergoing development have low permeabilities or low aqueous solubilities. However, the amorphous state is usually more soluble than its crystalline counterpart. The amorphous state has a higher Gibb's free energy, which can improve the apparent solubility but decrease the stability since the amorphous state tends to transform to the more stable crystalline form. Before recrystallization, a co-amorphous binary mixture's ingredients have to undergo a phase separation. The aim of this study was to obtain a better understanding of the amorphous-amorphous phase separation in co-amorphous binary mixtures and test the suitability of imaging Raman spectroscopy for detecting this phenomenon. To study the phase separation, we prepared three different 50:50 mass ratio binary mixtures of APIs: paracetamol-terfenadine, (PAR-TRF), paracetamol-indomethacin (PAR-IMC) and terfenadine-indomethacin (TRF-IMC). The binary mixtures were amorphized with melt-quenching and stored above their glass transition temperature (Tg) to monitor their phase separation. Thermal degradation was determined with a high performance liquid chromatography (HPLC) method to ensure that melt-quenching did not cause any thermal degradation of the molecules. Thermodynamic attributes (crystallization tendency, melting point (Tm) and Tg) were measured with differential scanning calorimetry (DSC) to ensure that the co-amorphous systems transformed to the amorphous state and remained amorphous after cooling and reheating. Phase separation was studied from the surface and cross-section (CS) with Raman imaging to examine if it occurred more on the surface than in the bulk. The Raman spectra were analyzed with principal component analysis (PCA) and Contour plots were produced from the PCA-score values to visualize concentration differences in the mixtures. The results showed that API vs API concentrations increased as a function of time in both surface and CS images before crystallization. This suggests that Raman imaging is a suitable technique to detect the phase separation phenomena in small molecule co-amorphous binary mixtures.