Proxy archives based on marine calcifying organisms and their element and isotope signatures represent valuable tools in the reconstruction of past climates. Despite the fact that the underlying biomineralization processes behind the measured signatures are poorly understood, these tools work remarkably well. However, even though they work well many researchers felt the need to decipher the “black box” and understand the processes leading to the measured signatures. In this paper we assess how far we have come in understanding the biomineralization processes underpinning proxy signatures derived from marine calcifying organisms and how this understanding improved the way we use these proxy archives today. Biomineralization in the context of proxy research is an interdisciplinary field and cross-discipline communication can be challenging due to a lack of background in foreign disciplines. This often leads to misunderstanding and over- (or under-) estimation of certain concepts/methods/data. We, therefore, present a concise introduction to the topic, clarifying key concepts and their applicability to proxy interpretation.