The settlement grew the way most São Paulo interior towns did. In 1848 the Simões family broke ground on the farm they named Pederneiras. By 1865 the settlement had joined the municipality of Lencois Paulista. Four years later it became a parish with the saintly name São Sebastião de Alegria. Then came the coffee century. Brazilian coffee plantations pushed into the state's interior throughout the late 1800s, and Pederneiras grew alongside them. In 1891 it broke away from Lencois Paulista and became its own municipality. In 1895, the town's residents restored the original flint-stone name, abandoning the saint's designation. The Judicial district remained elsewhere, however, which meant Pederneiras residents had to travel 35 kilometers to Lencois Paulista whenever they needed to go to court. They complained. In 1895 the district was moved to Jau, which was closer at 25 kilometers. Only in 1928 did Pederneiras finally get its own judicial district. The coffee economy had faded by then, and the town was ready for whatever came next.

About 70 percent of the rural area is used for sugarcane and cattle pasture. That percentage has held remarkably steady as the surrounding economy has shifted. The soil here is built on Bauru sandstone, with pockets of the fertile clay-rich soil locals call massapé. Citrus is expanding, which is part of a broader trend across the interior of São Paulo state as orange juice exports grew into one of Brazil's signature agribusinesses. The native vegetation is mostly gone. Eucalyptus and pine plantations have replaced it, a pattern repeated across the state. The climate helps. Summers are hot and humid. Winters are dry. Annual temperatures range from 16 to 34 degrees Celsius. For a population of roughly 47,000 residing in a tightly-clustered urban area with just 2,905 people in the rural districts, the farm sector punches well above its demographic weight. The town has always been more a processing center than a homestead community.

1975 changed the economic profile. Volvo selected Pederneiras for an industrial operation, and other metallurgical and mechanical companies followed. The town now produces truck and tractor parts for Volvo, Caterpillar, and Case. Pedertractor, one of the larger local manufacturers, makes electric motors, rotors, and stators. The Japanese conglomerate Ajinomoto arrived in May 2006, using the local sugarcane supply to produce export enzymes. This combination is unusual for a farm town of this size. Most São Paulo interior towns have specialized either in agribusiness or in manufacturing. Pederneiras has managed both, and the industrial sector provides steady wages that cushion the cyclical swings of commodity agriculture. The position at the geographic center of the state helps attract these investments. Trucks and tractors can reach most São Paulo markets from here within a day.

The Tiete River runs through the area and provides the hydrographic spine of the municipality. Smaller waterways feed into it: the Bauru, Veado streamlet, Agua Limpa streamlet, Patos streamlet, and the Pederneiras rivulet that runs through the urban area itself. The Tiete is the state's best-known river after the Paraná, and it carries the story of São Paulo's expansion inland from the coast centuries ago. Pederneiras borders a tight cluster of neighboring municipalities. Arealva and Bariri lie to the north, Boraceia, Itapui, and Jau to the east, Lencois Paulista and Macatuba to the south, Agudos and Bauru to the west. It has three districts of its own: Guaianas to the west, Vangloria to the south, and Santelmo to the north. The Nations Fair festival, held to mark the municipality's birthday, leans into the multicultural identity built by a century of immigration from Italy, Spain, Japan, and elsewhere. Different dishes, different shows, different national heritages meet at the town center. The flint stones still turn up in the fields.