For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co2+, Ni2+, and Cd2+). To thoroughly investigate this phenomenon we re-sequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile with those of its parental strain CH34. Genome comparison identified 11 indels (insertions and/or deletions) and 9 SNPs (single nucleotide polymorphisms) while transcriptomic analysis displayed 107 differentially expressed genes. Sequence data irrevocably implicated the transposition of IS1088 in higher Co2+ and Ni2+ resistances and altered gene expression, although the precise mechanisms of the augmented Cd2+ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk towards the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small non-conjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies.