Z-DNA, a left-handed isoform of Watson and Crick’s B-DNA, is rarely formed without the help of high salt concentrations or negative supercoiling. However, Z-DNA-binding proteins can efficiently convert specific sequences of the B conformation into the Z conformation in relaxed DNA under physiological salt conditions. As in the case of many other specific interactions coupled with structural rearrangements in biology, it has been an intriguing question whether the proteins actively induce Z-DNAs or passively trap transiently preformed Z-DNAs. In this study, we used single-molecule fluorescence assays to observe intrinsic B-to-Z transitions, protein association/dissociation events, and accompanying B-to-Z transitions. The results reveal that intrinsic Z-DNAs are dynamically formed and effectively stabilized by Z-DNA-binding proteins through efficient trapping of the Z conformation rather than being actively induced by them. Our study provides, for the first time, detailed pictures of the intrinsic B-to-Z transition dynamics and protein-induced B-to-Z conversion mechanism at the single-molecule level.