The ability to recognize the former existence of microbes as well as the biological origin of marine precipitates, such as putative microbialites, is crucial for understanding the development and history of early life on Earth. Increasingly, such rocks hold keys to understanding the geochemical evolution of the oceans and linked Earth systems. Vital trace elements previously have received relatively little attention as clues to the origin of carbonate rocks, and low abundance transition elements in particular, have been difficult to analyse in carbonate matrices for technical reasons. We have used laser ablation–inductively coupled plasma–mass spectroscopy for the in situ measurement of a broad suite of vital transition metals in Late Devonian reefal limestones that contain coeval microbialite (the calcimicrobe Renalcis), stromatoporoid sponge skeleton, early marine cement, and later diagenetic cement. Comparative experiments conducted in two different ion extraction modes determined theoretical detection limits for transition elements on NIST reference material SRM 612. Analyses of NIST glasses SRM 614 and 616 demonstrate accuracy relative to previously published data. On that basis we have identified significant enrichment of the vital elements V, Sn, Cu and Zn within the Renalcis. The stromatoporoid skeleton by contrast is enriched only in V. Earliest cements, which also may have been mediated to some degree by microbial biofilms on the basis of their morphology, show a much smaller degree of enrichment, and later cements show no enrichment, with the exception of Zn, which is concentrated in the latest cement. Fine particulate carbonate sediments (micrite) show variable metal enrichments that are attributable to varying contributions from detrital siliciclastic contamination. Renalcis was also enriched above the sponge and cements in regards to Mn, Cd, Co, and possibly Cr, but at less robust levels. Molybdenum and Sb were found not to be enriched in the Renalcis, and Ni, although clearly very low in concentration, could not be evaluated owing to its high detection limit. We additionally were able to identify specific zones of contamination in Renalcis encountered as the laser drilled deeper into the carbonate. Time resolved analysis allows exclusion of such contaminants from integration into the results. Successful application of the new technique will now allow us to assess metal uptake in ancient carbonates with implications for interpreting the biogenicity of putative microbialites.