Real-time delay between signals I currently have a real-time noise suppression algorithm based on two inputs from different microphones. It has passed most tests that I have thrown at it, however when the signal I am trying to retrieve has a slight delay one mic relative to the other it works poorly.

I have done preprocessing delay estimation in the input signal through cross-correlation just for testing and it works, however in the final algorithm I can't preprocess the signal as it is supposed to be real-time.

I am taking sub windows of signals and applying my algorithm, what I tried to do is apply the cross-correlation to each sub window, it takes the FFT of the sub windows does the calculation and then the IFFT just to get the delay each time. I later have to take the FFT of the sub window with a different windowing function for my filtering algorithm. This much extra processing will drastically reduce the sub window size my algorithm can keep up with in real-time.

The question is, is there a faster way to do this delay estimation? Maybe something that works with each input sample to get a better estimation each time? Something like a control loop? 

Thanks in advance!
I can't comment because I'm a new user... have a look to these questions:

Estimating the time offset (delay) between two audio signals in real-time

Generalized Cross Correlation

Time delay estimation of oscilloscope signals using cross correlation