Ribosomal proteins are a core components of the translational machinery. Yet, despite the ribosome’s complexity, conserved gene duplications are limited to a small subset of ribosomal proteins. We found only four bacterial proteins exists with such duplications, rpmE, rpmJ, rpmG, and rpsN , helping us to probe patterns of evolution and functional diversification. Comparative genomics revealed that rpmE and rpmJ co-duplications occur primarily within Gammaproteobacteria, whereas rpmG and rpsN co-duplications are largely restricted to Bacilli. For rpsN, encoding the universally conserved S14 superfamily protein, we identified analogous duplications in archaea and eukaryotes, with one eukaryotic paralog specifically targeted to mitochondrial ribosomes. Phylogenetic reconstructions indicate multiple, independent duplication events across these lineages. Notably, in several bacterial lineages one paralog retains a Zn²⁺-binding motif while its sister paralog lacks it, consistent with subfunctionalization under metal-ion availability. We generated time-calibrated trees, together with transcriptomic evidence, synteny, and nearby insertion sequence elements, support a model in which divalent zinc (Zn²⁺) availability acted as a selective axis shaping paralog retention and functional partitioning. Collectively, these results illuminate how metal-dependent specialisation, genomic context, and adaptive differentiation have contributed to the diversification of ribosomal proteins and, more broadly, to cellular and genomic complexity.