We present a flexible reverse microemulsion method using hydrophobic QDs for multiplexed encoded nanobeads encapsulating layers of different coloured quantum dots, called QD-“Onion”-Multicode bead (QOM). This novel system has monodisperse, photostable, and excellent luminescence properties that are stable at different pH values. The protection that the silica layers confer to the QDs allows them to be used as a ratiometric pH sensor by measuring the ratio of PL intensity of QDs from the different layers.