The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features reminiscent of enigmatic early fossil taxa combining complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused skeleton. This provides a unique opportunity to shed light on genomic mechanisms underlying the diversification of biomineralised armour. Using a high-quality whole-genome assembly and tissue-specific transcriptomics, we show that scale and shell formation in the Scaly-foot Snail employ independent subsets of 25 highly-expressed transcription factors, and illuminate potential genomic mechanisms for the nano-scale biosynthesis of iron compounds. Comparisons with other lophotrochozoan genomes indicate that the biomineralisation toolkit is ancient but expression patterns differ across major lineages. The ability of lophotrochozoan lineages to generate a wide range of hard parts, exemplified by the remarkable morphological disparity in Mollusca, draws on a capacity to dynamically modify the expression and positioning of toolkit elements across the genome.