Techniques are described for per-color adaptive in-pixel programmable gain amplification (PGA) for CMOS image sensors. The sensor has an array of photodetectors that each receives light through a corresponding color filter of a color filter array. Different color filters can have different transmissivity characteristics. Embodiments receive analog pixel output signals from the array of pixels. A respective gain select signal can be generated based on the signal level of each received analog pixel output signal to indicate a selected one of multiple gain factors. A programmable gain amplifier can be controlled, based on each respective gain select signal, to amplify the corresponding analog pixel output signal in accordance with the selected one of the predetermined plurality of gain factors, thereby generating a respective adaptively amplified pixel output signal. The adaptively amplified pixel output signal can be output to an analog-to-digital conversion path for generation of a digital pixel output signal.