In a desktop the motherboard controls the fans unless you have an alternative like fan control installed, so not windows.
In a laptop it's either still the motherboard, or a specific chip used to manage the fans and other peripherals (ie for Dell/XPS it's locked out of bios control and you need to use Dell's special software to adjust it; Fuck You, Dell!), so still not Windows.
Do you use windows?
I find that with windows the fan is always spinning, even if at low speed. While with linux most of the times it is not spinning at all.