In the present work, 11 different procedures for protein and metalloprotein extraction from horse chestnuts (Aescullus hippocastanum L.) in natura were tested. After each extraction, total protein was determined and, after protein separation through sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), those metals belonging to the protein structure were mapped by synchrotron radiation X-ray fluorescence (SRXRF). After mapping the elements (Cr, Fe and Mn) in the protein bands (ca. 33 and 23.7kDa), their concentrations were determined using atomic absorption spectrometry (ET AAS). Good results were obtained for protein extraction using a combination of grinding and sonication. However, this strategy was not suitable to preserve metal ions in the protein structure. In fact, there was 42% decrease on Mn concentration using this procedure, compared to that performed with sample agitation in water (taken as reference). On the other hand, when grinding and agitation with an extracting buffer was used, there was a 530% increase of Mn concentration, when compared to the reference procedure. These results indicate agreement between metal identification and determination in proteins as well as the great influence of the extraction procedure (i.e., the sample preparation step) for preserving metals in the protein structures.