A CMOS tunable-wavelength multi-color photogate (CPG) sensor is presented. Sensing of a small set of well-separated wavelengths (e.g., > 50 nm apart) is achieved by tuning the spectral response of the device with a bias voltage. The CPG employs the polysilicon gate as an optical filter, which eliminates the need for an external color filter. A prototype has been fabricated in a standard 0.35 μm digital CMOS technology and demonstrates intensity measurements of blue (450 nm), green (520 nm), and red (620 nm) illumination with peak signal-to-noise ratios (SNRs) of 34.7 dB , 29.2 dB, and 34.8 dB, respectively. The prototype is applied to fluorescence detection of green-emitting quantum dots (gQDs) and red-emitting quantum dots (rQDs). It spectrally differentiates among multiple emission bands, effectively implementing on-chip emission filtering. The prototype demonstrates single-color measurements of gQD and rQD concentrations to a detection limit of 24 nM, and multi-color measurements of solutions containing both colors of QDs to a detection limit of 90 nM and 120 nM of gQD and rQD, respectively.