Abstract Animal signals are dynamic traits that can undergo considerable spatial and temporal changes and that are influenced by factors such as age, health condition and interactions with both the abiotic and biotic environment. However, much of our understanding of signal changes throughout an individual's lifetime stems from cross‐sectional, often laboratory‐based, studies focused on visual and auditory signals. Longitudinal field investigations of temporal variation in chemical signals, especially in vertebrates, remain rare despite chemical communication being the most ubiquitous form of information exchange in the natural world. To remedy this, we conducted a unique, replicated field experiment to study the temporal signal dynamics in free‐living lizard populations on natural islands. Specifically, we collected scent marks from individually marked lizards across five populations during the spring of two consecutive years and analysed the lipophilic chemical composition of these scent marks. Our findings demonstrate that the overall scent mark composition of individual lizards changed over time, shifting consistently in both direction and magnitude from year to year among individuals and across replicate populations. Similar patterns were observed for the chemical richness and diversity of scent marks. Temporal variation in the relative proportions of three potentially socially relevant signalling compounds in lizard scent marks revealed a more complex pattern: α‐tocopherol remained stable over time, oleic acid decreased and the change in octadecanoic acid proportion was body size‐dependent. Together, our results provide novel insights into how individual vertebrate chemical signals may fluctuate across space and time. We discuss the potential causes of the observed temporal variability and its consequences for chemical signal evolution. Read the free Plain Language Summary for this article on the Journal blog.