The early Earth could only make minerals from what was plentiful
The earliest minerals, formed in stellar, nebular, asteroid, and primitive Earth settings, were dominated by relatively abundant chemical elements—hydrogen, carbon, oxygen, magnesium, aluminum, silicon, sulfur, calcium, titanium, chromium, and iron [1]. Think of it as cooking with a well-stocked pantry: if a few ingredients make up most of what's available, most dishes will use those ingredients. In the same way, the common rock-forming minerals are built from the elements that were everywhere, which is why they are common.
Rarity, then, is partly a numbers game. An element that makes up a tiny fraction of the crust has fewer opportunities to combine into its own mineral, and those minerals end up scattered rather than concentrated. A statistical analysis of mineral rarity found that crustal abundance does correlate with the number of common minerals an element tends to form—but, tellingly, it correlates negatively with the number of rare species [2]. In other words, abundant elements produce many common minerals, while scarce elements tend to produce minerals that stay rare.
Rare minerals need a process that concentrates scarce elements
Scarce elements don't usually get together on their own. Mineral diversification happened largely through the gradual selection and concentration of rarer elements by fluid-rock interactions—for example, in hydrothermal metal deposits, complex granite pegmatites, and agpaitic rocks [1]. These are settings where water or magma repeatedly moves and deposits material, acting like a sieve that gathers a dilute element into a small, rich pocket where it can finally form its own mineral.
The scale of this effect is striking: at least 4,583 minerals—about 81% of all species—arise through water-rock interactions, making Earth's hydrological cycle the single most important factor in boosting mineral diversity [1]. A separate line of evidence points the same way. When researchers grouped rare minerals by the elements they contain, they found that crustal abundance alone doesn't explain how many minerals an element forms; geochemical affinity—how strongly an element bonds with sulfur or oxygen—and the way a principal element disperses through geological processes also matter [2]. So rarity is not just about how much of an element exists, but about whether geology can gather it together.
Life and weathering create rare minerals too, but they aren't the whole story
Near-surface weathering and oxidation is the most common single setting for mineral formation, accounting for 1,998 species, and biological processes are linked to at least 2,707 mineral species, mainly through oxidative weathering [1]. Life, in other words, is a powerful rare-mineral factory. But the same survey cautions against overstating this: contrary to earlier estimates, only about 34% of mineral species form exclusively as a consequence of biological processes [1]. Many rare minerals can form without life, which matters for thinking about how mineral-rich a lifeless planet could be.
The survey also found that 3,349 mineral species—59.2%—are known from only one paragenetic context, meaning one kind of formation environment, while another 1,372 species are known from two [1]. A mineral tied to a single, uncommon setting is naturally going to be found in few places. That is the fingerprint of rarity: not a lack of atoms, but a lack of the specific conditions that assemble them.
How rare is “rare,” and does it stay that way?
By the standard measure, nearly half of all IMA-approved minerals have been reported from four localities or fewer, and these form a continuum with common rock-forming minerals rather than a separate category [2]. That continuum is important: “rare” is a matter of degree, and the same element can produce both ubiquitous and endemic minerals depending on setting.
There is also a caveat about discovery. A comparison of the number of endemic minerals found since 2000 with the number expected to be truly endemic suggests a divergence—some apparently rare species may simply be under-sampled rather than genuinely scarce [2]. So part of the answer to “why are most minerals rare” is geological, and part may be that we haven't looked everywhere yet.
Sources used in this answer
On the paragenetic modes of minerals: A mineral evolution perspective
Mineral diversity began with abundant elements, and rarer elements were concentrated mainly by fluid-rock interactions and then by biologically mediated oxidation and weathering, with water-rock interactions linked to about 81% of mineral species.
The Taxonomy of Mineral Occurrence Rarity and Endemicity
Nearly half of IMA-approved minerals are reported from four or fewer localities, and crustal abundance alone does not determine how many minerals an element forms—geochemical affinity and element dispersion also matter.