[n]Cycloparaphenylenes ([n]CPPs) are strained macrocycles, comprising only sp2-hybridized carbon atoms. In recent years, [n]CPPs have become of great research interest in the field of supramolecular chemistry since their special structure enables the formation of novel host–guest complexes. In this work, we investigate the gas-phase chemistry of noncovalent complexes of [10–12]CPP with the pristine fullerenes C76/78/84 and the endohedral metallofullerenes (EMFs) Sc3N@D3h-C78, Sc3N@D5h-C80 and M3N@Ih-C80 (M = Sc, Y, Lu, Gd). The [1 : 1] complexes with [10–12]CPP are detected as radical cations. The stability and charge distributions of these complexes are studied using energy-resolved collision-induced dissociation (ER-CID). Our results assess the size complementarity, the influence of fullerene symmetry and size as well as the role of the metal size inside the EMF on the binding affinity and complex stability. Two main trends in complex stability have been found: First, [10–12]CPP form more stable complexes with EMFs than with pristine fullerenes and second, all complexes of EMFs with the C80 skeleton show similar stability despite the different metal clusters encapsulated. Another major finding is the fact that [11]CPP is generally the most suitable host for fullerenes with a C76/78/80/84 skeleton. Considering the charge distributions, we observe the existence of two different fragmentation channels for complexes with EMFs where the radical cation is either located at the CPP or at the EMF: (1) [n]CPP+˙ + EMF and (2) [n]CPP + EMF+˙. This behavior allows a clear distinction of the cage isomers ([11]CPP⊃Sc3N@Ih-C80)+˙ and ([11]CPP⊃Sc3N@D5h-C80)+˙ in the MS2 experiment. The experimental results are accompanied by density functional theory (DFT) calculations of ionization potentials (IPs) and fragmentation energies. The computational results fully confirm the measured order of complex stabilities and explain the prevalence of EMF or CPP signals in the spectra by the trend in ionization potentials.