Small-angle X-ray scattering (SAXS) is an ideal technique for characterizing inorganic nanoparticles in biological specimens large enough to be representative of tissues. As tissues consist of complex mixtures of structures, identifying particular structural features from single-wavelength scattering data can be problematic. Synchrotron SAXS can supply element-specific structural information in complex samples, using anomalous scattering close to absorption edges. Anomalous dispersion is a secondary effect that produces relatively subtle changes in scattering patterns. In order to utilize this effect for anomalous SAXS analysis, stringent control of instrument performance is required. This work outlines the development of high-quality data collection and processing strategies for Fe K-edge anomalous SAXS on the ChemMatCARS beamline at the Advanced Photon Source (APS), Chicago, with an emphasis on intensity normalization. The methods reported here were developed during a study of iron-loaded mammal tissues, but could equally well be applied to other complex specimens.