Zachary Quinto's eyebrows are a thing of wonder. They sit on his forehead like cat's tails, arching and twitching as he speaks, lending everything he says a subtle emphasis. After a few minutes in their company, you become quite mesmerised by their expressive movements. It's not inconceivable that Zachary Quinto's eyebrows could have a successful Hollywood career all of their own.

So it seems a pity that the role for which Quinto is best known, the role that catapulted him to major box-office success, required these follicular features to be partly removed, covered by heavy make-up and painstakingly reapplied, hair by hair, in a process that lasted several hours. And all because Quinto is about to return to the big screen as the razor-browed Spock in the new Star Trek movie, directed by sci-fi wunderkind JJ Abrams.

It must have been odd, I say, to lose such a distinguishing part of his face.

"I know! Tell me about it," says Quinto. "It's an uncomfortable aspect of having to play the character, having to shave three-quarters of my eyebrows and maintain them every day plucking them – it's very painful and tedious."

There was a separate make-up artist who applied the famously pointy Vulcan ears and the whole process took "two hours and 45 minutes. So if we had a 6am call-time, I'd have to be there at 3am." And is he a morning person? "No, no," he grins. "Not at all."

Still, he's not complaining. At 35, Quinto is not quite a household name but his subtle, psychologically complex portrayal of Spock in the 2009 Star Trek film was highly acclaimed and the movie generated almost £250m worldwide, making it the highest-grossing film of the entire Trek franchise and winning it an Oscar (for best makeup). Quinto's Spock was praised by both critics and diehard fans.

Now Quinto is back, in the sequel, Star Trek: Into Darkness, which comes with all the whiz-bang 3D special effects, Imax and green-screen technology you could hope for. The opening scene features Spock in the centre of a live volcano. If anything, the pace picks up from there. But it is in the quieter, more reflective scenes that Quinto really comes into his own. He possesses an uncanny ability to imbue the half-human, half-Vulcan Spock with a sense of inner conflict.

"The reality is Spock has emotion but he just doesn't express it," says Quinto when we meet in a central London hotel room. He has a cold and is drinking lemon and honey but refusing to grumble in a most un-actorly way. There is a packet of Strepsils on the table between us that lies unopened for the duration of the interview. "For me, playing Spock was really about cultivating an inner life. As an actor, your nature is to emote, so it's a little counterintuitive."

He confesses that as a young boy, growing up in Pittsburgh, the son of a barber of Italian descent and an Irish-American mother, he was more of a Star Wars fan. "I was born the year the first movie came out," he says. "I only experienced Star Trek in reruns and frankly, I was never really engaged. I think it was beyond me."

Since then, he's gone back to the original 1960s television series created by Gene Roddenberry and rediscovered their genius: "The way he was using this world to create a discourse to draw on these allegories of current day society was pretty unique and special. I just don't think I was old enough or wise enough to understand that as a kid."

Roddenberry was also known for casting ethnically diverse actors and challenging the racial typecasting prevalent in so much TV programming at the time. Indeed, the Vulcan doctrine is "infinite diversity in infinite combinations" – a utopian vision of the future embodied by a peaceful coexistence among all forms of life.

This history of tolerance appealed to Quinto who, in 2011, came out as gay in an interview with New York magazine – one of the few Hollywood actors working in big-budget action movies to have done so. Although there had been speculation about his sexuality during his career to that point – Quinto rose to prominence playing the villainous Sylar in the TV sci-fi drama Heroes from 2006-2010 and later appeared in an off-Broadway production of Tony Kushner's Angels in America, set against the backdrop of the 1980s Aids epidemic – he had never before spoken openly about being gay.

The decision to do so, he says, was triggered by the suicide of a 14-year-old American high school student, Jamey Rodemeyer, who had been bullied for his bisexuality. Both Quinto and Rodemeyer had made short videos for the It Gets Better anti-bullying campaign. At that time, Quinto was "on the cusp" of coming out, "but I hadn't yet gone so far as to acknowledge or actually to declare myself as a gay man. And yet I made this video and danced around my own relationship to it."

When he heard Rodemeyer had killed himself, Quinto felt his own obfuscation was "a hypocrisy that I couldn't abide for myself. It was one step short of full authenticity and there wasn't the kind of integrity in that act that I need to live by, so I couldn't be silent any more."

He looks at me levelly, dark eyes unflinching. When he speaks, the words come out of him in an eloquent tumble, as though he is quoting an erudite professor. He never ums or aahs. He just seems to know, without having to assess it first, what he thinks. It's very Spock-like.

The day before we meet, Jason Collins, an American basketball star, has also come out as gay. Quinto believes it has got easier under Obama's presidency for high-profile people to do so without fear of opprobrium. He has been a vocal supporter and campaigner for Obama – the first time they met, Obama gave him a Vulcan salute.

"I think we're living in a time we'll look back on as having had the same energy and perspective as the civil rights movement," Quinto says. "I take pride in being one of the actors in one of the major blockbuster summer action movies who is openly gay."

Watch the trailer for Star Trek: Into Darkness. Paramount

Has he experienced homophobia?

"Sure. I've experienced homophobia, both within myself and within the industry and within the world at large. Of course. For all of these advancements that the gay community is making, I don't think that it's eradicated. It still exists, in a way that's palpable. I think we need to learn how to engage with it, how to work with it and how to metabolise it as a society because I think it's in all of us – the fear of being different, the fear of being unknown, the fear of judgment. And I think the only thing we can do is accept it. You can't fight it because fighting it feeds into it. Fighting it gives power to the opposition."

He says that, by and large, the reaction to his decision has been positive. JJ Abrams sat him down before filming started and told Quinto that "he was a supporter and he respected the way I handled it. He did it in such an inimitably classy way."

Does Quinto think he has missed out on any parts as a result of being gay?

"If I have, I don't know it and I don't care to know it because if anybody takes that position, I wouldn't want to work with them to begin with."

His mother Margaret, who had no idea her son was about to declare his sexuality to the world, is "very proud of me all round. She's come to accept me for who I am".

But it has been a long journey. When Quinto was seven, his father died of cancer. His mother returned to full-time clerical work to support Quinto and his older brother. Acting became Quinto's refuge.

"I think losing my father put me in a position where I needed an outlet for this trauma," he says now. "It started as a hobby and within a year or two of starting to perform, I felt completely at home and comfortable."

After high school (where he put in an award-winning turn as the major-general in Pirates of Penzance), he studied at Carnegie Mellon University, graduating in 1999 and heading for Los Angeles. His true love was the theatre but he realised, with Spockish prescience, that the industry was changing and he should carve out a screen presence for himself first. The move to LA, where he quickly landed parts in TV series including CSI, Six Feet Under and 24, was "a means to an end. I saw the value of leveraging that degree of notoriety".

"There was this kind of sea-change [in theatre]. It wasn't like it was in the 70s. When Meryl Streep and Al Pacino and John Cazale and all those incredible actors started their film careers, it was because they were recognised on stage and you couldn't be a movie star if you didn't prove yourself as a theatre actor. And it's completely the opposite now. Marketing a play has become, to all intents and purposes, the same as marketing a film."

Does he think it's a shame that acting has changed? "I think all of it's a shame frankly, I really do – the way that creative integrity has been devalued in favour of commercialism and reality television. So much of it is so trashy and so devoid of any kind of substance."

In order to redress the balance, Quinto runs his own production company, Before The Door Pictures. Last year, he produced and starred in Margin Call, a thoroughly excellent indie feature about the financial crisis. Several more films are in the pipeline.

Although he makes it clear he loved the experience of filming Star Trek, you get the impression that Quinto hankers after more serious roles. He recently played Tom Wingfield in Tennessee Williams's The Glass Menagerie, in a repertory run that is transferring to Broadway in September. I wonder if he feels a particular kinship with Tom, a repressed hero hell-bent on escape, who grows up in a small-town home without a father?

He nods. His brow furrows, the eyebrows knit together intensely. "The parallels between my personal life and the life of Tom Wingfield are staggering to me," he says. "Just on an emotional level [it] reinforces my belief that there are no mistakes in the world."

He sits back. The eyebrows rest. He's clearly an actor capable of great things. Or, as Spock might put it: of infinite diversity in infinite combinations.