An apparatus and an associated method is provided for waveguide spectroscopy of a sample inside a container. The apparatus may include a substrate with a window that is transparent at the wavelengths of interest and is coupled to the container holding a sample; a waveguide core of a material that is transparent at the wavelengths of interest located on an inner surface of the transparent window adjacent the sample, the waveguide core having a refractive index greater than that of the sample, an optical element configured to couple light into and out of the waveguide, and a light source and one or more detectors located outside of the container.