The establishment of matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) in routine microbial identification boosted many developments towards high-throughput applications, including bacterial typing. However, results are still controversial for different bacterial species. We aim to evaluate the suitability of MALDI-TOF MS for typing clinically relevant multidrug resistant (MDR) Klebsiella pneumoniae subsp. pneumoniae clones using routine conditions and a previously validated chemometric analysis workflow. Mass spectra of 83 K. pneumoniae clinical isolates representing major human MDR clones [11 sequence types (STs), 22 PFGE-types] recovered in Portugal and Spain during outbreaks and non-outbreak situations (2003-2012) were obtained from cell extracts (CE) and intact cells (IC), and analysed with different chemometric tools. We observed a highly consistent peak pattern among isolates from different clones either with CE or IC, suggesting a high degree of conservation of biomolecules analysed (a large part corresponding to ribosomal proteins). Moreover, the low degree of agreement between MALDI-TOF MS and other methods (from 34.9 % to 43.4 % of correct assignments for CE and from 40.8 % to 70.1 % for IC) corroborates the low discriminatory potential of the technique at infraspecies level. Our results suggest a low discriminatory power of MALDI-TOF MS for clinically relevant MDR K. pneumoniae clones and highlight the need of developing tools for high-resolution typing in this species.