We report the encapsulation of a homologous series of N-alkyl-N,N-dimethylamine N-oxides in a molecular container with bis[2]catenane topology. N-oxides with short alkyl chains are co-encapsulated with one solvent molecule. Elongation of the alkyl chain from R = methyl to pentyl produced the progressive compression of the guest. The hexyl N-oxide reduces its compression by being singly encapsulated. Longer N-oxides (R = octyl to decyl) had to fold to adapt to the capsule’s dimensions and also experience a progressive compression. The mechanically interlocked nature of the container and the polar functionalisation of its cavity are responsible for the assembly of encapsulation complexes in solution displaying high packing coefficients (0.65–0.70). The high energy conformations adopted by the alkyl chains of the bound N-oxides are deduced from NMR experiments and molecular modelling studies.