The soil matrix is the solid phase of soils, and comprise the solid particles that make up soils. Soil particles can be classified by their chemical composition (mineralogy) as well as their size. The particle-size distribution of a soil, its texture, determines many of the properties of that soil, in particular hydraulic conductivity and water potential, but the mineralogy of those particles can strongly modify those properties. The mineralogy of the finest soil particles, clay, is especially important.

Gravel, sand and silt are the larger soil particles, and their mineralogy is often inherited from the parent material of the soil, but may include products of weathering (such as concretions of calcium carbonate or iron oxide), or residues of plant and animal life (such as silica phytoliths). Quartz is the most common mineral in the sand or silt fraction as it is resistant to chemical weathering, except under hot climate; other common minerals are feldspars, micas and ferromagnesian minerals such as pyroxenes, amphiboles and olivines, which are dissolved or transformed in clay under the combined influence of physico-chemical and biological processes.

Due to its high specific surface area and its unbalanced negative electric charges, clay is the most active mineral component of soil. It is a colloidal and most often a crystalline material. In soils, clay is a soil textural class and is defined in a physical sense as any mineral particle less than 2 μm (8×10⁻⁵ in) in effective diameter. Many soil minerals, such as gypsum, carbonates, or quartz particles, are small enough to be classified as clay based on their physical size, but chemically they do not afford the same utility as do mineralogically defined clay minerals. Chemically, clay minerals are a range of phyllosilicate minerals with certain reactive properties.

Before the advent of X-ray diffraction clay was thought to be very small particles of quartz, feldspar, mica, hornblende or augite, but it is now known to be (with the exception of mica-based clays) a precipitate with a mineralogical composition that is dependent on but different from its parent materials and is classed as a secondary mineral. The type of clay that is formed is a function of the parent material and the composition of the minerals in solution. Clay minerals continue to be formed as long as the soil exists. Mica-based clays result from a modification of the primary mica mineral in such a way that it behaves and is classed as a clay. Most clays are crystalline, but some clays or some parts of clay minerals are amorphous. The clays of a soil are a mixture of the various types of clay, but one type predominates.

Typically there are four main groups of clay minerals: kaolinite, montmorillonite-smectite, illite, and chlorite. Most clays are crystalline and most are made up of three or four planes of oxygen held together by planes of aluminium and silicon by way of ionic bonds that together form a single layer of clay. The spatial arrangement of the oxygen atoms determines clay's structure. Half of the weight of clay is oxygen, but on a volume basis oxygen is ninety percent. The layers of clay are sometimes held together through hydrogen bonds, sodium or potassium ionic bonds and as a result will swell less in the presence of water. Clays such as montmorillonite have layers that are loosely attached and will swell greatly when water intervenes between the layers.

In a wider sense clays can be classified as:

Alumino-silica clays or aluminosilicate clays are characterized by their regular crystalline or quasi-crystalline structure. Oxygen in ionic bonds with silicon forms a tetrahedral coordination (silicon at the center) which in turn forms sheets of silica. Two sheets of silica are bonded together by a plane of aluminium which forms an octahedral coordination, called alumina, with the oxygens of the silica sheet above and that below it. Hydroxyl ions (OH⁻) sometimes substitute for oxygen. During the clay formation process, Al³⁺ may substitute for Si⁴⁺ in the silica layer, and as much as one fourth of the aluminium Al³⁺ may be substituted by Zn²⁺, Mg²⁺ or Fe²⁺ in the alumina layer. The substitution of lower-valence cations for higher-valence cations (isomorphous substitution) gives clay a local negative charge on an oxygen atom that attracts and holds water and positively charged soil cations, some of which are of value for plant growth. Isomorphous substitution occurs during the clay's formation and does not change with time.

The carbonate and sulfate clay minerals are much more soluble and hence are found primarily in desert soils where leaching is less active.