During intraoperative fluorescence navigation to remove various neoplasms and during pharmacokinetic studies of photosensitizers in laboratory animals, in many cases, the ratio of photosensitizer accumulation in the tumor and normal tissue can reach ≥10-fold, which inevitably changes their optical properties. At the same time, the tumor formation process causes various metabolic and structural changes at cellular and tissue levels, which lead to changes in optical properties. A hardware- software complex for the spectral-fluorescence studies of the content of fluorochromes in biological tissues with significantly different optical properties was developed, and it was tested on optical phantoms with various concentrations of photosensitizers, absorbers, and scatterers. To correct the influence of optical properties on the photosensitizer concentration analysis by fluorescence spectroscopy, we propose the spectrum-processing algorithm, which combines empirical and theory-based approaches.