Cross-section measurements employing the photon-ion merged-beam technique for photoionization and photofragmentation of ions of endohedral fullerenes Xe@C60 and Lu3N@C80 exposed to synchrotron-generated extreme ultraviolet light and soft x-rays are presented. A part of the required Xe@C60 material was synthesized with the production apparatus available at the Institute for Atomic and Molecular Physics (IAMP) in Gießen. A list of modifications to apparatus and production methods facilitated an increase in the endohedral yield by a factor of 30. Xe@C60 measurements were carried out at the synchrotron facility Advanced Light Source (ALS) at the Lawrence Berkeley National Laboratory (LBNL) in Berkeley. The current study extends previous efforts on single and double ionization of Xe@C60+ as well as fragmentation channels towards triple ionization with fragmentation of Xe@C60+ and towards double ionization with fragmentation of negative Xe@C60− ions in the photon energy range 60–150 eV. The relative cross-section data were normalized to absolute measurements either directly or the relative cross sections were scaled to match absolute cross-section data of pristine fullerenes in the respective channels at energies where the encapsulated xenon does not contribute. The excess cross section due to the encapsulated atom is determined by comparison of pristine and endohedral fullerene. The experimental results are compared to previously published measurements for Xe@C60+ double ionization.Relative cross-section measurements for Lu3N@C80 were carried out at the synchrotron facility PETRAIII of the Deutsches Elektronen-Synchrotron (DESY) in Hamburg. Prominent structures related to the carbon K-shell ionization threshold were observed in the energy range 280–330 eV. These resonance structures have been analyzed in seven product channels and are compared with previously known absorption spectra of several fullerene species. Unlike for Xe@C60, no signatures of the encapsulated atoms have been found particularly searching for the N-1s and Lu-3d thresholds in the energy ranges 390–435 eV and 1500–1700 eV. The carbon K-shell threshold seen in double ionization of Lu3N@C802+ is shifted by Δ E = (2.90±0.24) eV with respect to the carbon K-shell threshold in double ionization of Lu3N@C80+. The shift is explained by the difference in the Coulomb potentials of singly and doubly charged and Lu3N@C80. An outer endohedral fullerene radius R=(5.0±0.4) x 10−10 m is inferred. Comparison with Sc3N@C80 indicates that Lu3N has an identical influence on the C80 behavior at the carbon K-shell as Sc3N