Dual wavelength frequency-domain measurements of photon migration (FDPM) are conducted on filtrate samples obtained from an industrial centrifugation process designed to separate Escherichia coli cell debris from the inclusion bodies. FDPM measurements consist of detecting phase delay of intensity-modulated light at 670 and 820 (or 830) nm. Optical properties of isotropic scattering and absorption are obtained from the regression of phase delay data to the optical diffusion equation. We show that the corresponding intensity-based measurements alone cannot provide accurate and independent estimates for these optical properties. However, FDPM-derived scattering coefficients of filtrate solutions (primarily consisting of 0.1-0.2 mu m E. coli eel debris) are sensitive to similar to 1 vol % of added inclusion bodies (of 1-2 mu m size). The technique, theory, and future adaptation of FDPM as an on-line monitor to detect the loss of inclusion bodies in centrifugation following homogenization are presented and contrasted to conventional, intensity-based measurements.