We present the application of spectral emission imaging microscopy as a method to quantitatively map photo-nic properties from below the surface of strongly interacting photonic three-dimensional (3D) crystals. We ex-cite emission from emitters deep inside a photonic crystal and record the local emission spectra with microme-ter lateral resolution. The recorded directional emission spectra are modified by Bragg diffraction, which we use to determine the local stop-band attenuation, center frequency, and width. Assembling the values obtained into spatial maps yields detailed access to the distributions of the local photonic properties below the crystal surface. We demonstrate this approach by analyzing the emission from the fluorescent protein DsRed2 infil-trated inside self-organized 3D titanium dioxide inverse opals.