This summer she retired as reigning world sprint champion, and after winning gold in the Olympic keirin. But, Kira Cochrane discovers, her time in the saddle was often fraught, she used to self harm and she had a serious falling out with British Cycling

According to Victoria Pendleton, British Cycling has already sold off her bike. Some staff members will probably never speak to her again. She suspects they will be relieved not to have to deal with her any more. She tells me all this with a twinkly, tinkling laugh, the kind people adopt when they are trying especially hard not to sound bitter. The words ring in my head as I hang up the phone after our second conversation. I feel unexpectedly gutted. I had anticipated writing a fairly straightforward story about a champion – a complicated champion, yes, but one who had experienced familiar ebbs of struggle and glory on the way to Olympic gold at Beijing, followed by those wild, psychological battles in London, where she won gold in the keirin, silver in the sprint. Instead, the tale of Queen Vic feels much darker.

This hadn't come across so strongly at our first meeting. At that stage I had only been given the first half of her autobiography, Between the Lines, written with Guardian sports interviewer Donald McRae. This covered some difficulties in her path to Olympic success, but nothing too extreme or extraordinary.

Pendleton is immensely friendly when we meet at the St Pancras Renaissance hotel, London, with an openness people probably either find brilliant or totally unnerving. She is renowned for being nakedly emotional, sobbing when she loses – sobbing when she wins. "I'm someone who wears their heart on their sleeve," she says. "I find it hard to act other than the way I feel."

She is suffering from a throat infection, which flared up predictably in the wake of her Olympic training, so pops a few pills as we start. If some of her comments have an obvious, umbilical connection to past problems – she never bites a medal for photographers, she says, because it would be like "licking a handrail", reminding me of her compulsive teenage hand washing – well, none of it seems too troubling either.

What comes across from the start is her quest for approval, specifically from men. The more desperate she has been to achieve this, the more it seems to have pushed people away. We talk about her earliest memory, and she says it is probably of watching her father race. Max Pendleton was a star amateur cyclist when she was growing up, and the book begins with him riding away from her up a hill, as she struggles to catch him, with the words "he doesn't love me, he doesn't love me," beating through her head.

Her other earliest memory is of being on the back of a yellow tricycle, ridden by her father, alongside her twin brother Alex. When they were four, Alex was pricked by a wild rose thorn that caused blood poisoning; he then had leukaemia. The illness came on suddenly, she says, and she remembers the moment he was rushed to hospital with perfect clarity. Was she worried? "I was very worried." She began praying intently, night and day.

Alex recovered, but their parents continued to watch him carefully; Pendleton writes that she sometimes "had to fight to get noticed as much", although life was pretty rosy beyond that. She began cycling at six, on the back of her dad's tandem, then racing with Alex, aged nine. For years he and the rest of the field – the juvenile group went up to 16 – would usually beat her. But Pendleton pursued cycling anyway, because she just "wanted to be good at something," she says, with a note of desperation. "I was just, like, all I want to do is be really good at something. Really, really good at something, so people are vaguely impressed by me."

Pendleton in action in the velodrome. Photograph: Visionhaus

By her mid-teens she was beating Alex, and when they were 15, he gave up cycling, as their older sister Nicola had before. She uses an interesting phrase to describe this, writing that Alex "saw his chance and took it", as if he was escaping a kidnapping. Did she wish she had given up then, too? "At times I felt like, 'Ah, I wish I'd been first to get out,' and then I was like: 'No, but those two would have both quit anyway, and Dad would be left with no one to cycle with.'" Couldn't he have cycled alone? She laughs. "Yeah, I know! He had lots of friends to cycle with anyway."

But there was no giving up. She felt responsible for her father's mood. Did the pressure bother her? "Oh gosh, yeah." If she was invited out on a Saturday night by friends, it meant she wouldn't be properly rested for cycling, and she would "be filled with guilt," she says. "Should I go, shouldn't I go? I really want to, but no. I'll go with Dad, and I'll go to the race, because that's more important, keeping him happy, than it is keeping [a friend] happy, and yourself happy ... You know, I didn't have to do it. If I'd had the strength of character to say, 'Actually, no, I'm not going this weekend,' I would have done. But I didn't."

When she was 16, the national track team noticed Pendleton's talent, and she was invited to Manchester to ride at the velodrome. But she wasn't set on pursuing a track career yet. One of her most interesting qualities is her ambivalence about cycling. Where most champions seem powered by a blinkered obsession, she is much more clear-eyed. For instance, she fully recognises that sport is essentially entertainment, and finds this comforting. "When you're in that bubble, training in that environment, with all those personalities who want you to win so desperately ... You think it's life or death. It feels like if you don't win you're going to be hung, drawn and quartered."

But she remembers watching track cycling on television last year, "and I was like, this is the most ridiculous sport on earth. Riding around a wooden bowl, with a bike with no brakes ... And it was just like …" She takes a big sigh. "Aaaaaah, it doesn't mean I don't take the training incredibly seriously. But at the end of the day, it's just a bike race."

She arrived at Northumbria University to study sport science, and started going to the gym every day. By her final year she was spending a week each month training with the British cycling team in Manchester. It was a male-dominated environment, and it is clear she felt an unworthy outsider at first, training alongside the men's elite squad, including Chris Hoy and Bradley Wiggins. "I was like, 'Oh my God, I'm rubbish. I don't even know what I'm doing' ... It really didn't feel like I fitted in. Not that they made me feel that way – the guys were always very friendly, but I did feel like a complete novice."

In 2002, she came fifth in the sprint at the World Cup in China. Not long afterwards she went to train at a sprint academy in Aigle, in the Swiss Alps, under French cyclist, Frédéric Magné. "Within the first two weeks," she says. "I thought I was going to die. My eyes were totally sunk in the back of my head. I had bags under my eyes. I was so tired. I was like: how do people do this for a living?"

As the months went on, she began to doubt herself. She felt she needed to work on her core strength, and began to exercise outside her prescribed training programme. This angered Magné. "I had always feared letting down figures of authority," Pendleton writes, "my dad most of all, and so I felt diminished by disappointing Fred."

She had started cutting her arms with a Swiss Army Knife, and as their relationship deteriorated she continued. "I'd been training really hard," she says, "and my progression had been very slow ... I just dwelled on the negativity of being stuck in that little room in Switzerland, by myself, feeling like a failure ... Thank the Lord, Steve Peters came along, because if I hadn't met him, I think I probably would have left Switzerland, and given up."

Peters, a psychiatrist, had been sent out to see her by British Cycling; the two connected instantly. So much so, he apparently introduced her once to his students as his "greatest success". He gave her "some options," she says. "'You are in control of this Vicky. You do have the power, and the ability, to retrain the way you think right now, and get out of this situation'."

Pendleton headed home in 2004, before a disappointing first Olympics in Athens, where she came ninth in the sprint. But it wasn't long before she hit a winning streak, claiming the world championship in the event the next year. She has won nine world titles altogether, six in the sprint. Then, in 2006, she met Scott Gardner, an Australian performance analyst who had joined the British team, and after a frosty start, they fell in love.

Both knew this wasn't allowed; a relationship between a member of the coaching staff and an athlete was considered unprofessional. "We knew Scott would lose his job," she says, "so that was an accepted part of us deciding to go on a date for the first time."

Once they had decided they were serious, they told Shane Sutton, head coach at British Cycling; he and Dave Brailsford, the performance director, agreed the relationship should be kept quiet in the buildup to Beijing. There, at the Games, Pendleton rode to triumph, confirming her position as a towering champion, the best female sprinter in the world.

It should have been a moment of celebration, but all she felt was "deadened incomprehension", she writes. And these feelings didn't improve over the next few days. Sutton and Brailsford decided the news of her relationship with Scott had to come out.

With boyfriend Scott Gardner after winning silver in the sprint this summer. Photograph: Andy Stenning

This was the part of Pendleton's book I had reached when we first met, but I knew some of what happened afterward: the fallout from the revelation of their relationship, Scott having to leave his job. I just couldn't work out what was behind the continuing rift with the team's staff. After she won her medals at the London Olympics this summer, for instance – medals that marked the end of her cycling career – she and some of the senior staff didn't even exchange proper goodbyes.

One was Jan van Eijden, her full-time sprint coach, the man responsible for holding her on the bike at the start of each race. They had a great working relationship before she became involved with Gardner, so it was difficult to understand why he would be so angry. Towards the end of her book though, the chronology breaks, as she reflects back on the night after she won her gold medal in Beijing. At this point, parts of the picture become clearer.

Van Eijden had just found out about her relationship with Gardner, and the three were having a furious row. "I was so shocked at the severity of his reaction," she tells me, when we speak again over the phone. "I thought he might be a bit annoyed, but the fact that he was literally raging, livid, was shocking. He was disgusted in what we'd done, thought we were unprofessional, disrespectful and we'd betrayed him. All these words which, personally, for me, they're not words that people use. Because I'm not that kind of person. I'm very by the book, you know? I don't like breaking rules. For someone to describe my character, and Scott's character, in such derogatory terms, was very hurtful."

She was so upset that she found a pair of nail scissors and cut herself in front of the two men. I wonder if, after this, some staff were scared of her. A colleague who reacts to a row by cutting themselves is someone you might be both worried for, and wary of. When I suggest this, she says she doesn't "think anybody knew about it apart from Jan". Perhaps that's true, but it's the sort of story that has the potential to spread quickly around a workplace, particularly one where psychology is so central. "I don't think anyone will know until they read it," she says, "if they read it."

Has she had any reactions to the book yet from the team? "No, I don't imagine they'd speak to me any more, anyway, to be honest. I'm not imagining I'll have much contact with them. As it is, they've sold my bike already." She is close friends with some of the team, but there are certain key members, "who I am sure will be very happy not to have to deal with me ever again, and I think they'd probably be quite open about expressing that too. And I don't blame them, because if I've hurt them with my actions, I can't change it. It's something I'm going to have to live with, and I'm sorry it caused people such distress. But I'm in love with Scott, and I wouldn't change that. I'm very happy with him."

The hardest part was "if it had been any other kind of job, I might have been able to change organisations, and carry on doing the job somewhere else. But I had no other options. I can't change nationality, and I wanted to represent Great Britain." There were times when her relationship with Van Eijden was so bad that she almost felt: "I don't want to win because he takes the credit for it, and really I don't feel he's part of my performance, any more, in some respects. But I would never do that, because I would never compromise my end result. But these thoughts would run around my mind sometimes, when I was feeling particularly low."

She is "pretty worried" about the book coming out, she says. "Because I have been fairly open and honest about a lot of issues – but I haven't told any lies … I was worried about British Cycling being annoyed that I've kind of, well, not talked them down, but haven't necessarily portrayed them in a glowing light ... For so many years I've had to talk about how amazing the programme is, and how well supported I am, and at times I haven't really felt 100% supported by that, but it's my job, it's what I have to say. And I'm still performing, so people are like – well, why are you still producing gold medals then, if it's so bad? It makes for a very difficult situation, and I don't want to be coming across as the whingy whiner, but I'm the only one to complain, so no one else has a problem."

"I don't think that I'm a particularly complicated person to work with," she says. "But I'm not a robot. And if they've learned anything, I hope they've learned that they need to approach working with the girls in the team a little bit more sensitively than they have in the past. Because if everything I've been through has done that then it's been a success. And it would be nice that it's been worth it in the long run, because I do feel that somewhere that a lot of sports, and my sport in particular, fall short is the level of support for the men and the women is so different. They seem to know what men need, but they don't really seem to understand how to get the best out of the women."It can't help that so few of the senior staff are women. "There's nobody with any power, female," she replies bluntly. "And they need that, in my opinion."

Pendleton is such a mixture of parts; a rock and indie kid, with a Smashing Pumpkins lyric tattooed on her wrist, who also revels in fashion. She says it's going to be liberating, to do whatever she wants, "and not feel responsible! The only person I'm going to let down is me, if I don't do very well at my next job. I'm just going to have a whole year of trying new stuff." She plans to marry Gardner in 2013, and after that she'll start thinking about a serious career choice. "I've always had this one thing overriding my lifestyle since I was nine. I have never missed a racing season since 1989. Having a year to make up for all that commitment is not unreasonable."

She loved her Olympics experience this year, despite the disappointment of disqualification in the team sprint, and relegation in the first race of the individual sprint final too. When she won gold in the keirin, she says she felt: "Oh, I'm so happy right now. This is amazing. I sung the national anthem, because I would anyway, but it was the only thing that stopped me from blubbering completely on the podium".

It would have been so easy to leave the self-harm material out of the book. It's not as if she's short of drama. But she says she wanted to send a message to other people that you could have problems like these, get past them, and succeed. "I'm not the perfect model of what an athlete should be, mentally or physically," she says, "but I've worked very hard to be as close to that as I possibly can, and it's taken time, effort and practice. It's not something that comes naturally, I wasn't born with it ... If you're willing to work, you can be better. You can be the best, there's nothing stopping you." The question is, would you want to?