Probe encapsulated by biologically localized embedding (PEBBLE) has emerged as a new type of sensing technique for complex systems. Generalized ratiometric PEBBLE nanosensors prepared by encapsulating an intensity-based probe and an inert reference dye inside the pores of stable matrix possess advantages of easy synthesis, immunity to interference, lower toxicity, and robustness to variations in probe loading. However, the selection of appropriate reference dyes used in generalized ratiometric PEBBLE nanosensors is a rather difficult task since they should satisfy some stringent requirements. In this contribution, the feasibility of using carbon dots (C-dots) as generic inert references in synthesizing PEBBLE nanosensors was first investigated in detail. And a dual-wavelength monitoring strategy and the quantitative fluorescence model for generalized ratiometric probes (QFMGRP) were adopted to solve the problems brought by the use of carbon dots as inert references. C-dots doped PEBBLE nanosensors (C-PEBBLE nanosensors) for the quantification of NO2- and free Ca2+ were synthesized by encapsulating C-dots and intensity based fluorescence probes (i.e., acriflavine for NO2-, and Rhod-2 for Ca2+, respectively) inside the pores of stable matrix. Experimental results showed that the combination of C-PEBBLEs, the QFMGRP model and the dual-wavelength monitoring strategy achieved accurate quantification of NO2- and the free Ca2+ in real-world samples. Their quantitative results were in good consistence with those determined by HPLC and atomic absorption spectrophotometer, respectively. The strategies proposed in this contribution have generic applicability in the synthesis of PEBBLE nanosensors and their quantitative applications.