Andy Warhol’s films, which tested the endurance of audiences and made icons out of the marginalised and dissolute, altered profoundly the nature of cinema. Much of the work which bore his name from the late 1960s onwards, however, was made by the writer-director Paul Morrissey, who has died aged 86. “Warhol is a trade term,” said Morrissey. “Like Disney.”

About his famous friend and collaborator he could be comically scathing. “He didn’t have many points of view,” he said in 1996. “He didn’t have many ideas at all, actually. Maybe three. If he made a choice, it was almost always the worst possible choice in the world.”

Stephen Koch, the author of Stargazer: The Life, World and Films of Andy Warhol (1991), called the two men “mutually incompatible talents … Morrissey utterly blind to the refined complexity of Warhol’s experience of the world; Warhol wholly incompetent to assemble the often beguiling commercial product Morrissey sells under Warhol’s name.”

The first decade or so of Morrissey’s career was given over to orchestrating and managing projects under the Warhol name: not just the films but the stewardship of the avant garde rock pioneers the Velvet Underground (whom he had brought to Warhol’s attention) as well as the launch in 1969 of the influential magazine Interview, which Morrissey co-founded. It sometimes seemed as though the rest of his life was spent fighting to have his contribution recognised.

Morrissey was also Warhol’s personal manager from 1965 to 1974. Asked what this entailed, he said: “I had to think of things that he might do, I had to do them, and then I had to pretend that he was involved.” The two men met in the early 60s when they were both showing their work in New York. After Morrissey had assisted on, and co-directed, Warhol’s films for several years, a turning point arrived in 1968 in the shape of the camp western Lonesome Cowboys.

“Before that, I had been helping Andy make the kind of movies he wanted to make, which was the kind of movie which looked like nobody had made it,” Morrissey said in 1978. “Lonesome Cowboys was the first time we were making an effort.” The characters, including gay gunslingers, were still bickering and flirting and talking about their hairdos, as they had always done, only now they were doing it outdoors in Arizona, wearing costumes and riding horses, rather than lounging around in ratty Lower East Side apartments. This combination of tones and styles (timeless genre conventions side by side with a modern, spaced-out looseness) introduced a new piquancy.

Morrissey achieved his most striking results with the acute, funny and freewheeling trilogy of Flesh (1968), Trash (1970) and Heat (1972). Each showcased the sullen, swaggering beauty of Morrissey’s discovery Joe Dallesandro (immortalised as “Little Joe” in Lou Reed’s song Walk on the Wild Side), alongside “Warhol superstars” such as Viva and Jackie Curtis, and the transgender actors Candy Darling and Holly Woodlawn.

The pictures presented a compassionate portrait of outsiders struggling to make and maintain emotional connections. The great director George Cukor declared himself “lost in admiration” and even instigated a campaign, ultimately unsuccessful, to land an Oscar nomination for Woodlawn for her performance in Trash.

The plots of these movies were threadbare – Flesh, shot over the course of five Saturday afternoons, follows a hustler trying to drum up the money for a friend’s abortion – and sometimes second-hand. Heat, for instance, partially recycles Sunset Boulevard. But it was the attitude that counted, as well as the ambiguity over whether the films constituted art or reality. Though the performances could be affectless to the point of mundanity, Morrissey was adamant about the dividing line between cinema and life. “If a person is in front of a camera, they’re acting,” he said. “It’s not possible to live in front of a camera. What I always believed in was the truthfulness of artificiality.”

Born into an Irish Catholic family in New York, Paul was the son of Joseph, a lawyer, and his wife, Eleanor, and he remained a devout Catholic all his life. He was educated at Fordham preparatory school and Fordham University, where he began making 16mm films.

His first short depicted a priest saying mass on the edge of a cliff before throwing the altar boy to his death. Another, Civilization and Its Discontents, featured “a hood in a pea jacket strangling a fat albino” while Like Sleep showed two drug addicts nodding off. These brought him to Warhol’s attention and led to his involvement on films including My Hustler (1965) and Bike Boy (1967). His first feature-directing credit, shared with Warhol, was on the three-and-a-half hour, split-screen Chelsea Girls (1966). It was precisely the formalist experimentation of that film which some Warhol loyalists accused Morrissey of betraying when he manoeuvred the artist’s brand toward the ordered narratives of Hollywood melodrama.

While Warhol was recovering after being shot by Valerie Solanas, founder and sole member of the Society for Cutting Up Men (SCUM), Morrissey assumed full creative control over the films – or, rather, his creative control over them was finally made explicit. After Flesh, Trash, Heat, and Women in Revolt (1971), which included a send-up of SCUM in the shape of PIGs (Politically Involved Girls), Morrissey moved in a different direction. Taking Dallesandro with him, he made a pair of kitsch, gory but technically accomplished horror films in Italy: Flesh for Frankenstein (1973) – released in the US as Andy Warhol’s Frankenstein – and Blood for Dracula (1974). “I’m always a little afraid of getting stuck doing one thing,” he admitted.

No one could accuse him of that. Flesh for Frankenstein was shown initially in 3D, so that a man whose hand is sliced off seemed to bleed all over the stalls, his guts wobbling in the audience’s faces on the end of a sharpened pole.

Morrissey’s next film, The Hound of the Baskervilles (1978), was even more unlikely: a madcap take on Sherlock Holmes starring much of the British comedy establishment, including Peter Cook, Dudley Moore and Kenneth Williams, as well as the theatrical giant Joan Greenwood, who remarked of Morrissey: “He’s a dear, really, but the first few days one didn’t know where one was. One got used to him. He’s jolly clever.” Critics were less impressed: Time Out magazine remarked that “a first-year film student would be ashamed”.

He continued making films, including Forty Deuce (1982), starring Kevin Bacon as a hustler, and Mixed Blood (1984, aka Cocaine), about Hispanic drug dealers in Manhattan, and spent most of the rest of his life talking about, and clarifying his part in, the Warhol story.

He remained throughout his career proudly rightwing, outspokenly moralistic and wholly indignant, railing against everything from drugs – “There’s no difference between a person using drugs and a piece of refuse” – to method acting: “When you see people like Daniel Day-Lewis and Ralph Fiennes screaming and hyperventilating, you’re seeing the phoniest kind of bad acting. You may as well have a ‘men at work’ sign. It’s not acting if you can see it.”

Despite the marginal nature of much of his work, he was at heart a populist. “I’m very traditional about everything,” he said. “I like action, comedy, pretty colours, pretty people. Art is a formula any idiot can manage. Competing in the marketplace is the only challenge left.”

He is survived by his brother, Kenneth.