The nonsense-mediated mRNA decay (NMD) pathway was initially identified as a surveillance pathway that degrades mRNAs containing premature termination codons (PTCs). NMD is now also recognized as a post-transcriptional regulatory pathway that regulates the expression of natural mRNAs. Earlier studies demonstrated that regulation of functionally related natural mRNAs by NMD can be differential and condition-specific in Saccharomyces cerevisiae. Here, we investigated the regulation of MAC1 mRNAs by NMD in response to copper as well as the role which the MAC1 3′-UTR plays in this regulation. MAC1 is a copper-sensing transcription factor that regulates high-affinity copper transport and is activated under low copper conditions in S. cerevisiae. We discovered that MAC1 mRNAs are regulated by NMD under complete minimal (CM) but escaped NMD under low and high copper conditions. Mac1p-regulated genes escape NMD in conditions where MAC1 mRNAs are NMD sensitive. We also found that the MAC1 3′-UTR is the NMD targeting feature on the mRNAs, and that MAC1 mRNAs lacking 3′-UTRs were stabilized during copper deprivation. Our results demonstrate a mechanism of regulation for a metal-sensing transcription factor, at both the post-transcriptional and post-translational levels, where MAC1 mRNA levels are regulated by NMD and copper, while the activity of Mac1p is controlled by copper levels.