De Heem was born in Utrecht as Johannes van Antwerpen. He studied first under his father David de Heem the Elder (1570–1631), then under Balthasar van der Ast. His "middle name", Davidsz, is a patronym referring to his father's name: In Dutch a name ending in -sz is like -son in English and Mac- in Scottish, meaning "son of" the rest of the name. He lived in Leiden from about 1625 to 1629, where he studied in 1629 under David Bailly (1584- c. 1657). His professional name, "de Heem", means literally "the home".

He moved to the Southern Netherlands and joined the Guild of Saint Luke of Antwerp in 1635 or 1636 and became a burgher of that city in 1637. However he was often absent, as attested by the duties he had to pay for this. His remarkable talent gained him a considerable reputation. He could hardly satisfy the demand. De Heem was considered one of the greatest painters of his time. He was well paid and a portrait of Prince William III surrounded by a cartouche of flowers and fruit was sold for 2000 guilders, one of the highest prices ever paid for a painting during the Dutch Golden Age. His sons worked together with him in his workshop on the commissions for new paintings. He retouched their work and put his signature on the paintings.

He remained in Antwerp until 1667, when he moved back to Utrecht, where records trace his presence from 1668 to 1671. He left Utrecht in 1671 when French troops were approaching the city. It is not known when he finally returned to Antwerp, but his death there is recorded in the guild books.

Van Heem married twice, first with Alette van Weede with whom he had three surviving children on her death in 1643, one of which, Cornelis, would become a still life painter. He married a second time in 1644 with Anna Catherina Ruckers with whom he had six more children, one of whom was Jan who would also become a still life painter.

Apart from his two sons, he had several apprentices: Michiel Verstylen, Alexander Coosemans, Thomas de Klerck, Lenaert Rougghe, Theodor Aenvanck, Andries Benedetti, Elias van den Broeck, Jacob Marrel, Hendrik Schoock and Abraham Mignon.