Metal and precious stones, used to create tools, vessels, and jewelry, were mostly found in the deserts of Egypt. Mining was an exhausting, dirty, and dangerous activity. Because most mines were in the desert, living conditions were difficult, so mining was seasonal. Traveling overland to the mines was avoided. Slow caravans of donkeys were hard to supply and needed a large protective force against bandits.

Ancient mines were small spaces that were not enlarged and supported with timbers like modern mines. Workers had to lie on their stomachs swinging picks all day. The workers were usually paid in food and drink and were not allowed to keep even the smallest piece of gold or jewel. During the Roman period, mining was done by slaves who were prisoners of war or convicts. Mines were also worked by poor families, including the children, who crawled into small spaces and brought out broken rock.

Copper and gold were the most commonly mined metals in Egypt. Iron was occasionally found in its meteoric form, but was not mined by the ancient Egyptians. Tin, which was used with copper to make bronze, was not mined in Egypt either. It was imported from Syria.

King Djoser conquered the Wadi Maghara region, where copper ore was mined beginning in the Third Dynasty. During the Middle Kingdom, copper ore in the Eastern Desert became available. By the Eighteenth Dynasty, the Egyptians controlled the copper mines in the Sinai desert, Timna, and other locations in the Arabah Valley. Copper ore contained about 10 to 12 percent copper; crucibles found at mines suggest that extracting the metal included some refining at the mining site.

Gold was mostly found in the Eastern Desert and Nubia. Gold mines in Wadi Hammamat and Wadi Allaqi were used beginning in the Rammesside period. The silt from running water also formed natural gold deposits underground. This gold was collected by washing away the lighter sand particles and then melting the remaining gold particles.

In gold mining, foremen were aware of the directions of gold-bearing quartz and only mined as long as was justified. After the rock was collected, it was heated to make it brittle. Women then crushed the stone in mortars and grinders. The crushed material was washed out on basalt tables with grooved ceramic tops or over stretched sheepskins. The lighter sand washed away while the gold remained in the grooves. This technique was used only in places near deep wells; otherwise the rock was taken to panning locations along the Nile.

Semiprecious stones were also mined in Egypt. Amethyst, which occurs in shades of purple and violet, was mined in the eastern desert near Aswan and in the western desert near Abu Simbel. From the deserts also came carnelian, which varies from dark brown to light brown, and a kind of carnelian called chalcedony that is translucent and light green in color. Light blue feldspar was mined in the eastern desert. Turquoise deposits were mined near Serabit el-Khadim. The Egyptians excavated large galleries in the sandstone, supported with pillars with reliefs of the pharaoh carved into the rock at the entrance. During the winter rainy season, water was conducted into the mine to extract the turquoise stones. The site was mined until about 1000 BC.

The ancient Egyptians also mined salt for cooking from deposits in the western desert or from evaporation pools on the Mediterranean coast. Natron, sodium bicarbonate, was an important material used for mummification, glassmaking, and to preserve food. It was found in a deposit in the Wadi al-Natrum halfway between Cairo and Alexandria. "Southern natron" was found at el Kab. Alum, used in the textile dyeing process, was mined from the oases of Dakla and Kharga in the Western Desert. Gebel Rasas was the source for galena, a type of lead used in cosmetics.