When I reported from war zones for this newspaper, I used to warn local people that it was bad luck to say they hoped to see me again. If I came back, it would mean their country was in crisis.

In 1999 and 2000 I returned repeatedly to Kosovo, first under Slobodan Milosevic's increasingly brutal Serbian regime, then after Nato and Russian forces occupied the territory and found themselves struggling to curb reprisals by the Albanian majority against their former oppressors. For all the country's natural beauty, my memories of this corner of the Balkans, slightly smaller than Northern Ireland, were of burning homes and bloodshed. To this day, I have been to more funerals, both Orthodox and Muslim, in Kosovo than anywhere else in the world.

Yet here I was in 2013, back again, this time as a tourist. At last I could linger to admire the alpine scenery, which once caused a war photographer to curse that the place "looked like goddamn Switzerland", making his pictures unsaleable. ("The cows even have bells around their necks!" he complained.) I would be able to visit the ancient Orthodox monasteries on which Milosevic based his claim that Kosovo was inalienable Serbian territory, and sip macchiato – makiato in Albanian – in the pavement cafés of what is no longer Pristina to its inhabitants but Prishtina, capital of an independent nation.

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Not that this was any conventional holiday. I was travelling with Nicholas Wood, once a colleague and rival who covered the Balkans for the BBC and The New York Times before going into the travel business, setting up a company called Political Tours. His clients are people who spurn beaches and country cottages in favour of investigating the world's more troubled regions in much the same way that a journalist would.

For a week some dozen of us would be in and out of meetings with ministers, impoverished rubbish-pickers, diplomats, uprooted Serbs and hip Albanian fashion designers and media types. Often there seemed to be as little time for a makiato as when I was on deadline.

But that was just the way my companions liked it. "I have been interested in the Balkans for some time and wanted to understand the conflict here," Robert Murphy, an American oil-company executive based in Singapore, told me. Several, including the remarkable Jo Rawlins Gilbert, an 83-year-old former probation officer from California, had travelled with Wood before, in her case to Libya. (She has also been recently to Afghanistan – three times – and Iraq.)

Garry Hay, a retired supermarket logistics manager from London, had been with Political Tours to Bosnia, while Mark Sugi, a Californian surgeon, was looking forward to his next trip with the company, to North Korea. By comparison, Kosovo was beginning to look positively soft.

It was here, though, that Nicholas Wood got the idea for his company. An American traveller he had enlisted as a relief driver while covering the territory's dash to independence raved about the experience, and launched the journalist on a new career. While he relies on other experts to lead his tours in countries such as South Africa and Russia, in Kosovo there is no need. He has watched the country's emergence from war and ethnic cleansing to relative stability, but for me the changes felt more abrupt.

In January 1999, I visited Brezovica, Kosovo's only ski resort, and found burnt-out chalets and deserted hotels and restaurants. It has always been a Serb-majority area, which had to be protected from Albanian reprisals after Nato arrived. But in 2013 the roadblocks had long disappeared. The slopes are sprouting new holiday homes as Prishtina's elite colonises the resort, and more ski lifts have been added. Two guides, Igor Nikolcevic, a Serb, and Arben Islami, an Albanian, could talk about what united them: their passion for the Shaar mountains, where bears, wolves and eagles are still to be found.

Going through the mountains to Prizren in a tour bus was much less terrifying than my midwinter drive 14 years ago, when snow chains had no effect on a road surface of polished ice. And the former Ottoman capital of Kosovo, a Unesco World Heritage Site for its stone architecture, was considerably more relaxed than when I interviewed terrified Serb refugees in an Orthodox seminary protected by German troops. We met the courtly Veton Nurkollari, who has put Prizren on the map for a different reason. He is the organiser of DokuFest, a documentary film festival which takes over the town every summer. In 11 years it has grown into one of the most important of its kind on the festival circuit. Many of the films are shown in the open air, including in the stone fortress that looms over Prizren, and the partying goes on far into the night.

Not that it is possible to forget what happened here not so long ago. All along the road from Prizren, below the aptly named Accursed Mountains that separate Kosovo from Albania, there are monuments to some of the bitterest fighting of the war. (It has to be said that they are not very tasteful: one statue of a fallen hero is known as "the air guitarist", because the rifle he is supposed to be holding was never added, for reasons unknown.) Italian peacekeepers still guard the 14th-century Decani Orthodox monastery, with its amazingly well-preserved frescos, because of the occasional flare-up.

We were shown around by the abbot, Father Sava Janjic, to whom we journalists always used to turn when we wanted to hear from a Serb who was not a raving nationalist. During the 78 days of Nato bombing in 1999, when Milosevic's death squads were seeking to drive Albanians out of Kosovo, he sheltered dozens of them at the monastery. It is sad that he still needs protection from Serb-haters when anyone is free to visit Kosovo's other great medieval Orthodox monastery, at Gracanica.

Just after Nato arrived, you had to go through two sets of roadblocks to enter this Serbian enclave, just over the hills from Prishtina. No longer: while there has been an flurry of new building all over Kosovo, sweeping away the destruction I remember, nowhere is it more pronounced than around the capital. Now it is hard to tell where Prishtina ends and Gracanica begins, forming a metropolis where the youthful crowds washing in and out of bars and clubs remind you that half the population of 1.7 million is under 25. An art installation says "NEWBORN" in giant 10ft letters, and that seems to sum it up.

We were told at numerous briefings that any veneer of prosperity in Kosovo was almost entirely due to international aid and remittances from Kosovars working abroad, but this could not entirely dispel the spirit of optimism we encountered. It even survived a visit to Kosovo's most downtrodden community, the Roma, discriminated against under both the old regime and the new. In squalid Neighbourhood 29, near Prishtina, we saw the work of the inspirational Elizabeth Gowing, a former teacher in Hackney, London, who launched the Ideas Partnership, a project enabling Roma children to get an education and their mothers to earn a living other than by scavenging in rubbish tips.

A trip to Mitrovica showed the newcomers in our party what Kosovo used to be like. The northern town has been frozen in confrontation since 1999, when French peacekeepers closed the main bridge over the Ibar River to keep the Serbian and Albanian inhabitants apart. A few months later, I narrowly escaped a beating by a crowd of Serbs who claimed I was a spy for the Kosovo Liberation Army, and in 2013 tensions were still running high. Diehard Serbs had dumped mounds of rubble at their end of the Ibar bridge to keep "intruders" at bay, with huge Serbian flags hanging above. They were unsettled, we were told, because talks were beginning in Brussels over the future of the enclave, and the Serbs were as fearful of a sellout by Belgrade as a takeover by Prishtina. It was a relief when we left the aggression behind and returned to the relative normality of the rest of Kosovo.

Political Tours has had to address claims that what it does is a form of voyeurism, an accusation sometimes levelled at war correspondents as well. But nobody could fault the seriousness of my travelling companions, who raised enough in a whip-round to pay two months' rent for the Ideas Partnership project. It would be quite possible to have an enjoyable holiday in Kosovo without worrying about local politics: you could see the monasteries, hike and ski in the Shaar mountains, paddle down the Drini River, stay in a kolla stone tower in the beautifully restored village of Dranoc and enjoy the excellent restaurants of Prishtina. But you would not have got under the skin of the country as we did.

"I remember seeing Kosovo on the news every night, with green night-vision film of bombs and missiles flying," said surgeon Mark Sugi. "I knew nothing about the ethnic cleansing until we got here, though. That's why I opted for this tour – to meet people on the ground. It was an opportunity to learn something about the world." At a time when news organisations lack the budgets to send correspondents to far-flung places, and rely increasingly on "user-generated content", maybe it is just as well that some people are going to see for themselves.

Having been in Kosovo during the worst of times, for me the journey was something like an exorcism. The country remains volatile, and faces a mountain of problems, but finally I can take away some happier memories. And when Kosovo's people expressed the wish that I would return, I could say I hoped so too.

Travel essentials

Getting there

Raymond Whitaker travelled with Political Tours (0843 289 2349; politicaltours.com), which offers an eight-day tour of Kosovo from £2,600, excluding flights. The next trip runs 15-22 March 2014. Tailor‑made tours are also available on other dates. Germania (flygermania.de) operates direct flights from Gatwick to Prishtina twice a week.

More information

The Ideas Partnership (theideaspartnership.org)