For weeks, Sarah Perry has been petitioning the heavens for a clear evening so that she can show me her telescope in action, but tonight the skies over Norwich are cloudy. I must content myself with looking at the instrument at rest and noting that it’s a big bit of kit, not remotely the kind of thing you just shove up against your eye. By most people’s standards, Perry is a serious astronomer – she has a tattoo of Halley’s comet below her heart – although she would probably counter that she doesn’t have the mathematical ability to undertake in-depth research. Nonetheless, the fact that she has discussed these matters with the Italian theoretical physicist Carlo Rovelli and thanks him in the acknowledgments to her new novel, Enlightenment, tells you that she’s not exactly a slouch.

“I said to him, ‘I love the ideas of physics so much, I read and watch lectures and do my little calculations when it’s within my capacity, but I can’t do the maths.’ And he told me that he loves music, Bach in particular, but he can’t read music. He said, ‘I love the music and I understand music, I just can’t read the score, and that’s what it’s like for you. You love the physics, you grasp it, you understand it, you just can’t read the score.’ And it was so moving.” She pauses. “And it meant that I didn’t have to go and do A-level maths!”

With a rueful glance at the telescope, she whisks me off to the sitting room of the house she shares with her husband, Robert, and a trio of animals: Ruby (a saluki), Janey Morris (a whippet) and Mrs Hudson (a cat), all three of whom lie on the sofa near and occasionally on me. A fire burns in the grate and to eat there are homemade Strict Baptist tarts like those that appear in Enlightenment, at the chapel in which the novel is partly set (“a kind of sweet iced tart nobody ever saw elsewhere, and which was as particular to Bethesda as the hymns and the harmoniums”).

In what will come as little surprise to those who have followed Perry’s career from her debut novel After Me Comes the Flood to the bestselling tale of myth and science The Essex Serpent and the disturbing, gothic-inflected Melmoth, Enlightenment is a novel about the presence and absence of faith. It also draws more directly on her own life in its portrayal of a Baptist community in the fictional town of Aldleigh, a version of Chelmsford, in Essex, where Perry and I grew up.

Geographically, the setting wasn’t entirely deliberate, she tells me. On a recent trip to Chelmsford, “I decided to walk around the parts that I suspected were Aldleigh, and they were all there in a way that made me shiver, almost. So there’s the railway arches from Chelmsford railway station, and there’s a couple of pubs nearby the railway stations that have been synthesised into one. And there’s Ebenezer Strict Baptist chapel, where I spent an enormous part of my childhood and youth, the river, the traffic lights outside the chapel. It would be easy to think that my setting something in Essex or Chelmsford, or East Anglia, was a conscious choice. But actually, it’s just the matter at hand. It becomes a natural location for my imagination.”

The branch of Baptist faith that Perry belonged to is Calvinist in its belief that God has selected a finite number of souls – the elect – who will be granted salvation, and that the Bible is God’s infallible word. (Perry recalls a preacher telling the congregation that it is a Haynes manual for the human being.) Adherence to the doctrine is a way of proving your love of God, involving baptism by immersion and the rejection of worldly temptations such as contemporary culture in the form of television and pop music. Perry left the church in 2007, when she was in her late 20s, in part galvanised by its opposition to same-sex marriage and after a lengthy period of doubt.

As a child, I walked past the Ebenezer Strict Baptist chapel with my mother on our way into town, dimly aware that it had a more old-fashioned and forbidding aspect than my jolly Sunday school. But it’s almost impossible for an outsider to imagine the realities of Perry’s upbringing within the religious community that she left as a young woman. Is that what made her want to write about it?

“It comes back to this long process that I went through, over the course of the years of writing this book, of locating a truthfulness and a sense of integrity in what I was writing about,” she tells me. “It would be an act of, I think, cowardice and almost deceit, to never write in some way about the most important formative ideas, places and years of my life.” Like Thomas, one of the novel’s two main protagonists, whom we follow from middle into old age, Perry had to reckon with a split in her consciousness that left her both outside the church but still deeply affected by it. She explains that she retains “a deep love for the fabric of the buildings, for the hymns, for the scriptures, for the people, for much of the teaching. I have one toe in the sea and the remainder of my body on a more worldly shore, but I’ve never completely left. I don’t think I ever can completely leave.”

* * *

One of the consequences of an upbringing that marks you out as different to most of those around you is that you are frequently asked about it. In the early days of her writing career, Perry says, people would bring up Jeanette Winterson and ask her if it had been like Oranges Are Not the Only Fruit. The recollection makes her laugh: “The idea of my quiet, godly mother drinking herself into a stupor and then belabouring me with a pan is just funny.” Doesn’t it also give you something to react to, or against? “There’s a mischief in me when I write, and I really like provoking and surprising readers and ideally winding them up. And I think there is something quite provocative about writing about a kind of background that a liberal, contemporary, secular reader would assume would have been in some way devastating to the psyche, and show that a) all upbringings are devastating to the psyche, and b) there’s also enormous comfort and consolation. It’s rarely as easy as turning your back on it and running for the hills and never looking back. It’s not been my experience.”

In Perry’s case, leaving the church – as does the other main character in Enlightenment, the teenager Grace Macaulay – has not led to a rupture with her family, to whom she remains close; indeed, her father, also a keen astronomer, helped her to plot out cometary orbits when she was working on the celestial elements of the book. But there are serious theological ramifications, the most significant of which is that in turning away from God, she is providing evidence that she is not one of the chosen, and will therefore suffer an eternal penalty.

We have been eating cake, fussing dogs (“Janey Morris, stop it!” she cries, when the whippet burrows into my lap) and talking about interior decoration – her house combines a love of the Arts and Crafts movement with the kind of whimsy that favours a lavatory pan imprinted with blue-and-white windmills – and now we are talking about hell. Does she really mean it? “My closest loved ones who are still in the church would absolutely hold to Protestant, reformation theology, Calvinism, which would say that before the foundation of the world, God knew who would be saved, and who would not be saved, and they would hope that I would be among the elect. And if I’m not, then I will go to hell.

“I carried Ebenezer chapel round, like a snail in its shell,” she says, and she is certain that “if I had stayed in the church, I would not have been able to be a novelist”; the level of scrutiny, though “very kind”, was too intense. When she was 17, she remembers, she had layers cut into her hair, and then went off to Bible study; when the man leading the group noticed, he changed the subject of the lesson to Jezebel. She has been at great pains to emphasise the goodness of her fellow Baptists, but I wonder whether there is also a degree of anger.

“I felt and still do feel a kind of grief that I’ve never been free,” she replies. “Now, to what extent anyone is free I don’t know. But I’m 44 and I’ve never done anything without somebody in some form of position of authority or presence in my life knowing that I’ve done it. So I married very, very young and I’ve never lived alone. For the first few years of marriage I would have believed biblically that I was subordinate to my husband. And so what I’ve never had is freedom. I do feel sad about that. And I wonder what I might have been had I ever felt free.”

This is quite a revelation from a woman who – in her conversation, her bearing, her work – seems liberated, even audacious, and definitely comical. Her husband, who pops in to stoke the fire, is like nobody’s idea of an authoritarian. She jokes about meeting people who tell her that they, too, had an old-fashioned childhood and thinking: “Buck up matey, you’ve got no idea!” But the complications of her worldview are clearly genuine, and the impact on her visceral. She tells me that, “I woke up the other night frightened that Enlightenment dishonours God, a form of God I no longer worship. And I was moved to deep shame and fear that I have written a book that is dishonouring to God.” Is she frightened of the sin itself, or of a punishment that might follow? “Because of itself: because for so much of my life, I loved God. And there’s parts of me now in which that goes round and round like an echo that never fades.”

It’s fascinating to wonder how this has affected Perry’s development as a writer. Her lexicon is heavily influenced by religious writing, and she knows that when she did her MA in creative writing it bewildered some of her cohort. “I think there was a feeling and perhaps there still is a feeling that my writing was imitative of Victorian literature. And that’s not the case. The fact is that my influences, and my world, were Victorian.”

I recall being at a literary festival after The Essex Serpent had come out in 2016 and Perry was deep in conversation with a fellow writer, explaining with immense enthusiasm and erudition why he should read Tennyson’s In Memoriam. He was listening intently, but there was a frisson in the air around them. When he left, and she was immediately asked what they had talked about and what he was like, she inquired politely who that had been. It was Suede’s frontman, Brett Anderson.

When Apple TV+ filmed The Essex Serpent, adapted by Anna Symon and directed by Clio Barnard, Perry was an extra, and became, as a dressmaker herself, particularly interested in the costume department. She enjoyed the entire process of watching experts perform their expertise, but was not fazed by proximity to celebrity in the form of Claire Danes and Tom Hiddleston: “The joy that I got out of it was seeing two people who were bloody good at their job do a really good job on my work, rather than a feeling of being closer to the limelight. It meant that I didn’t feel particularly overawed or overcome by speaking to them, because thinking of celebrities as being coated in gold hadn’t been part of my upbringing.”

In terms of writer-level celebrity, Perry achieved some of it herself in the aftermath of The Essex Serpent – and its readership will no doubt be delighted that Cora Seaborne makes a return of sorts in Enlightenment. Cora’s creator, though, feels as though she’s left the novel behind, not least because it coincided with the period in which she became ill and was diagnosed with the autoimmune condition Graves’ disease. In a weakened state, she also ruptured a disc in her back, leading to months of what she describes as “tormenting pain”. It was that time of distress and suffering, she feels, that partially explains the much darker turn she took in Melmoth.

But like her other East Anglian novel, Enlightenment has much of the yarn about it; the narrator as the teller of a tall and unlikely tale, slightly out of time, slightly otherworldly. There are, as always, jackdaws – the gothic corvids that she has adopted as a form of familiar. She explains that she is in the process of making peace with the kind of novel she writes: big, filled with ideas, propulsive.

“There’s a certain terminology around the kind of literature that will always pop up on best books of the year, say: it’s very taut, very spare, as if it’s a woman who’s expected to be very thin. People write about books as if they’re women’s bodies: slender, there’s barely anything there. And I don’t write like that. I can’t. I don’t live like that. For a little while, I thought perhaps I ought to give it a shot. And it was like writing for a year with my left hand. It was just painful and terrible. So I then came to terms with the fact that this is how I write, and how could I not when I was raised reciting reams of the King James Bible and reading Shakespeare for fun? I’m not going to suddenly write frictionless prose with no speech marks.”

• Enlightenment is published by Jonathan Cape on 2 May. To support the Guardian and Observer, order your copy at guardianbookshop.com. Delivery charges may apply.