<p>Origin determination is crucial for foods under Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI), where risks of fraud are high. Authentication of fruit origin in cake fillings is particularly challenging, as pulps lose distinctive morphological traits during transformation, new ingredients are added, and for the same fruit variety the genetic information is independent of the geographic origin. Minerals, intrinsically linked to soil and environmental conditions, represent promising tracers of geographical origin. This may be disguised by the minerals present in the different technological ingredients added in manufacture of the cake fillings. This study hypothesized that even in these conditions, elemental profiles can serve as markers of fruit origin. For this, industrial apple (<i>Malus domestica</i> L. var. ‘Golden Delicious’) and pear (<i>Pyrus communis</i> L. var. ‘Rocha’) cake fillings from different orchards origin and the correspondent fresh fruit were analyzed by inductively coupled plasma–mass spectrometry. For apple samples, the geographic origin can be distinguished by the content of nine elements: B, La, Cs, Ce, Cr, Rb, Cu, Tl, and Mn, after the removal of Fe, Sr, Ba, Al, Pb and Zn, associated to the processing of the cake fillings ingredients. For pear samples, the geographic origin can be distinguished by the content of eleven elements: Zn, Cu, Ni, La, Pb, Rb, Mn, Co, B, Ba, and Cs, after removal of Fe, Cd, Ce, Al, Sr, Cr, and Tl. These elements, characteristic of soil, environment, and depth of tree roots, can be used as markers of authenticity of the fruit cake fillings.</p>