As an important raw material for the confectionery industry, the cocoa bean (Theobroma cacao L.) has to meet certain legal requirements in terms of food safety and maximum contaminant levels in order to enter the cocoa market. Understanding the enrichment and distribution of essential minerals but also toxic metals is of utmost importance for improving the nutritional quality of this economically important raw food material. We present three X-ray fluorescence (XRF) techniques for elemental bio-imaging of intact cocoa beans and one additional XRF technique for quantitative analysis of cocoa pellets. The interrelation of all the methods presented gives a detailed picture of the content and 3D-resolved distribution of elements in complete cocoa beans for the first time.