J. C. Jacobsen moved his brewing out of the crowded city in 1847, looking for better water and more room, and secured a royal licence for the site. He named it for his son Carl. The main building, inaugurated in 1853, is the one now known as the Carlsberg Academy; a fire gutted the works in 1857 and the buildings went back up the same year.

Father and son did not get along. In 1870 Jacobsen extended the site with an annexed brewery and leased it to Carl; ten years later, after further disagreements, he terminated the lease, and Carl simply built his own brewery next door. With his father's grudging consent he called it Ny Carlsberg, New Carlsberg, which forced the original to become Gammel Carlsberg, Old Carlsberg. The two operations competed side by side for a quarter of a century before merging in 1906 under the single name Carlsberg Breweries. Carl ran the combined company until his death in 1914.

In 1875 Jacobsen founded the Carlsberg Laboratory, and the following year he created the Carlsberg Foundation to fund it, allocating some of his brewery shares to the endowment. It is the most consequential thing he ever did.

In 1883 the laboratory's Emil Christian Hansen worked out how to isolate a single strain of pure yeast. The organism was named Saccharomyces carlsbergensis, and every lager yeast in use today descends from it. Before Hansen, fermentation was a gamble against wild contamination; after him, it was reproducible chemistry. In 1901 Søren Peder Lauritz Sørensen took charge of the laboratory's chemical department, and in 1909, while studying how hydrogen ion concentration affected proteins, he proposed a logarithmic scale for acidity and called it pH. He held the post until 1938.

When Jacobsen died in 1887 the Foundation inherited the rest of the brewery, and it still controls the company today under a voting structure written into his will.

Carl Jacobsen spent money on the brewery the way other men spent it on palaces. The Elephant Gate of 1901, designed by Vilhelm Dahlerup, carries a red-tiled tower on the backs of four granite elephants, borrowing openly from Bernini's elephant and obelisk on the Piazza della Minerva in Rome. The tower has a floor area of only 115 square metres; it was a water tower and a herb silo. Dahlerup's earlier Dipylon Gate of 1892, named for the Greek term for a double gate, doubled as a malt chamber and a clock tower, and the clock still runs.

There is a lighthouse here too, the Lime Tower of 1883, built from Faxe limestone and lit by electricity a year after the technology reached Old Carlsberg, among the first places in Copenhagen to have it. And there is a 56-metre chimney that Carl commissioned from Dahlerup specifically to prove that an industrial chimney could be beautiful. It winds upward under Egyptian lotus motifs, with replicas of the Notre-Dame chimeras crouched on its plinth, looking out over the city.

Carlsberg announced in July 2006 that production would move to Fredericia in Jutland, leaving only the headquarters and the small Jacobsen specialty brewery on site. An international competition drew 220 entries, and in May 2007 a small Danish practice called Entasis won it. The plan took the Best Master Plan award at the 2009 World Architecture Festival in Barcelona.

Entasis deliberately ignored the conventions of modern development. Instead of towers in parkland, the scheme borrows from medieval city centres: short narrow streets, alleyways, unpredictable turns, many small squares. Nine slim high-rises between 50 and 120 metres mark the most important of those spaces. Roughly 600,000 square metres are being built out, about half of it residential, some 3,000 homes. Carlsberg's kilometres of underground cellars are part of the plan, some opened up as strange public rooms, others left buried. Carlsberg station opened in July 2016; a European School was inaugurated on 29 November 2018. The old mineral water factory is now Dansehallerne, 9,000 square metres given over to contemporary dance.

On 16 February 1868 Hans Christian Andersen came to dinner at J. C. Jacobsen's house and wrote it up afterwards in his diary. "It was like a wealthy country home abroad," he noted, marvelling at the machinery for hoisting food up from the kitchen, the gas in the stoves, the wax candles in the lamps. That house is the Carlsberg Academy now, its two-storey dining hall still ringed by Bertel Thorvaldsen's Alexander Frieze, its English-style garden of 1848 still full of rare trees Jacobsen carried home from his travels.

The garden survived because the site was protected before the machines arrived: in 2008, thirteen building complexes and a garden were listed. That is the unusual thing about Carlsberg. Industrial sites are usually erased or embalmed. This one is being lived in.