In Enterobacter cloacae, the genetic lesions associated with derepression of the AmpC β-lactamase include diverse single nucleotide polymorphisms (SNPs) and/or indels in the ampD and ampR genes and SNPs in ampC, while diverse SNPs in the promoter region or SNPs/indels within the coding sequence of outer membrane proteins have been described to alter porin production leading to carbapenem resistance. We sought to define the underlying mechanisms conferring cephalosporin and carbapenem resistance in a collection of E. cloacae isolates with unusually high carbapenem resistance and no known carbapenemase and, in contrast to many previous studies, considered the SNPs we detected in relation to the multilocus sequence type (MLST)-based phylogeny of our collection. Whole-genome sequencing was applied on the most resistant isolates to seek novel carbapenemases, expression of ampC was measured by reverse transcriptase PCR, and porin translation was detected by SDS-PAGE. SNPs occurring in ampC, ampR, ompF, and ompC genes (and their promoter regions) were mostly phylogenetic variations, relating to the isolates' sequence types, whereas nonsynonymous SNPs in ampD were associated with derepression of AmpC and cephalosporin resistance. The additional loss of porins resulted in high-level carbapenem resistance, underlining the clinical importance of chromosomal mutations among carbapenem-resistant E. cloacae.