An improved method for non-invasively measuring a concentration of a target analyte dissolved in a fluid flowing through a sample is presented. It includes directing a probe beam of electromagnetic radiation, consisting of time multiplexed components of different wavelengths, through the sample and measuring the difference of the absorption of the radiation at at least one wavelength pair at different sample states. During sample state changes, the amount of fluid containing the target analyte within the sample is changing, which varies the total amount of target analyte in the sample, as well as the absorption properties of the sample. The sample states are produced, for instance, by compressing and uncompressing the tissue sample. The accuracy of the presented method is enhanced by including continuous estimation of the amount of the fluid containing the target analyte within the sample, and measurement of the variations of the absorption at a wavelength at which the target analyte absorbs significantly. The method is particularly useful in measuring the concentration of a target analyte, such as glucose, in tissue containing blood. An apparatus for performing this method also is disclosed.