Three-dimensional Brillouin confocal microscopy is an imaging modality that correlates with mechanical properties in biological media from subcellular to tissue level. Over the years we developed new approaches to this technique that improve the spectral performance and can measure directly the local refractive index as well as the complex modulus of the sample; to achieve this goal, we probed two co-localized Brillouin scattering geometries. The confocal microscopy setting ensures three-dimensional mapping with high resolution, while the back scattering configuration allows access to the sample from the same side. For these reasons, such an instrument constitutes a new approach in investigating biological phenomena providing both local index of refraction and mechanical information with a single measurement. This technique has been improved in speed and spatial resolution in order to be applied to some specific challenging material characterization such as liquid-liquid phase separation.