Heterochrony, or variation in developmental timing, is a widely recognized source of phenotypic novelty. While many studies have investigated the phenotypic effects of heterochrony over evolutionary timescales, the phenotypic effects of newly emerged (heterokairic) variation in developmental timing remain poorly understood. We leverage a wild population of the facultatively paedomorphic salamander, Ambystoma talpoideum, to understand if and how reordering the timing of metamorphosis relative to sexual maturation generates novelty in the amphibian skin microbiota. We demonstrate emergence of phenotypic novelty in the heterokairic (paedomorphic) life stage. This includes novelty that is both intermediate to and more extreme than ancestral (larval, metamorphic) life stages. Further inspection shows that novelty in the skin microbiota comprises both individual novel microbes and novel microbe combinations and emerges due to both microbial gain and microbial loss. We discuss the eco-evolutionary implications of our findings for both HA microbiota and phenotypic spaces more broadly.