Biological systems remain unperturbed (are robust) in the face of certain genetic and environmental challenges. Robustness allows exploration of ecological adaptations. It is unclear what factors contribute to increasing robustness. Gene duplication has been considered to increase genetic robustness through functional redundancy, accelerating the evolution of novel functions. However, recent findings have brought the link between duplication and robustness into question. In particular, it remains elusive whether ancient duplicates still bear potential for innovation through preserved redundancy and robustness. Here we have investigated this question by evolving the yeast Saccharomyces cerevisiae for 2,200 generations under conditions allowing the accumulation of deleterious mutations and put, for the first time, mechanisms of mutational robustness to test. S. cerevisiae declined in fitness along the evolution experiment but this decline decelerated in later passages suggesting functional compensation of mutated genes. We resequenced 28 genomes from experimentally evolved S. cerevisiae lines and found that mutations accumulated more in duplicates than in singletons, and this enrichment of mutations was found mainly in genes that originated through small-scale duplications. Genetically interacting duplicates showed similar selection signatures and fixed more amino acid replacing mutations than expected. Regulatory robustness of duplicates was supported in our experiment by a larger enrichment for mutations at the promoters of duplicates than at those of singletons. Analyses of yeast gene expression under different environmental conditions showed larger variation in duplicate’s expression than that of singletons under a range of stress conditions, sparking the idea that regulatory robustness allowed exploration of a wider range of phenotypic responses to environmental stresses, hence faster adaptations. Our data provide strong support for the persistence of genetic and regulatory robustness in ancient duplicates and for the role of this robustness in the evolution of adaptations to various stresses.