A hand-to-mouth existence is nothing new in Portuguese football. Outside the power of os três grandes of Benfica, Porto and Sporting, lies a desert of indifference. In this commercial wasteland pitiful attendances are commonplace, with attendances below 1000 registered in 13 top-flight matches in 2010-11.

The feelgood factor from Euro 2004, a tournament that generated so much national pride, quickly began to fade. This season União Leiria moved out of their own Euro legacy, the €50m, 30,000-capacity Estádio Dr Magalhães Pessoa, unable to afford the rent and overheads having never filled it during eight-and-a-half years of residence. They now play in the modest, 6,000-capacity Estádio Municipal in nearby Marinha Grande. Towards the end of April, 16 of the first-team squad rescinded their contracts after going months unpaid and the team started a subsequent league match against Feirense with just eight players. After finishing bottom of the table, Leiria failed to meet the entry requirements for the Liga de Honra (second division), so prepared for semi-professional life in the regionalised third tier under a new board.

Yet official Portuguese Liga statistics make the club the 11th-best supported in the country. In 2010-11, 11 of the Liga's 16 clubs averaged gates below 5,000, with five of those averaging less than 3,000. Yet the problem isn't restricted to provincial Portugal. The rot has long since spread to the big cities. Perhaps the least surprising development in this direction was in early spring 2011 when the perpetually broke Estrela Amadora, the club from the Lisbon suburbs that produced Manchester United's €8m signing Bebé, finally closed the doors of the Estádio da Reboleira for the last time. 

The Estrela president António Oliveira made public his hope that a charitable windfall from their former charge's move to England would have saved them, given that Bebé had been at Guimarães for only six weeks before the United deal. In truth, that would have been an act of benevolence too far. He had joined the northern club from Estrela on a free transfer granted in lieu of unpaid wages. Bebé had frequently been subbed a few hundred Euros by his agent here and there to get by. Neither he, nor Guimarães, owed Estrela a debt.

If this slow death was relatively predictable, the fall into ruin of Belenenses and Boavista has been even more painful to watch. In a country in which there is no denying the hegemony of os três grandes, these two clubs stand out as, remarkably, the only clubs outside that clique to have been crowned champions since the Liga was first arranged in its current round-robin format in 1938.

Situated back from the River Tejo, some 8km to the south of Reboleira, the Estádio do Restelo feels almost too prestigiously situated to be home to a football club, above and beyond even the positioning of the Santiago Bernabéu on the power vein of the Paseo de la Castellana in Madrid. The sense that this is the case is further accentuated by Belenenses's current problems.

The 1946 champions have spent the last two seasons struggling near the foot of the Liga de Honra. At the club's annual general meeting in summer 2011, president António Soares warned that "bigger gate receipts alone won't resolve our problems. These problems need new solutions and personally, I don't think we'll manage to get out of this situation without new partners." Haemorrhaging money and playing in front of dwindling crowds, gravity means that the club's privileged geographical position is today more of an anomaly that a genuine advantage.

That hasn't always been the case. Visitors to Belém, the fashionable and picturesque suburb in which the club is based (Os Belenenses meaning 'the ones from Belém') don't have to go far to spot the very genesis of the club. Some 70 metres from the entrance to the presidential palace, on the opposite side of the road, is a stone bench engraved with the legend Aqui nasceu o CF "Os Belenenses" 23-9-1919 — Belenenses was born here on 23 September 1919. Collating the club's illustrious origins and restricted present, a short stroll 50 paces to the west of the bench brings you to the town's club shop, a tiny green kiosk with enough space for the shopkeeper to have just about enough elbow room to open a newspaper in quiet periods. 

If the shop emphasises that the club has become a niche concern, the presidential palace gives clues to something that was more than a football club in pre-democracy Portugal, and Belenenses's strength meant something in the thirties, forties and fifties. "At this moment in time Portugal was governed by a dictatorship," said Carlos Manuel Pereira of the Lusa news agency. "The history of Belenenses was closely tied to that of the military. Various generals in turn served as club presidents and they gave the club strength and visibility both nationally and internationally." 

Belenenses had played on the Campo do Pão de Fio, a modest green off the Rua de Belém, the suburb's main street, facing the Tejo — and on the edge of which the club's kiosk now symbolically rests. The team was often displaced in its early years, frequently playing on a site in Lumiar, where Lisbon's international airport stands today. In January 1928 it gained a solid base in Belém, setting up at the Campo das Salésias. Estádio do Restelo was built on the existing site to replace it and opened in 1956. 

Permanence in Belém had been a big factor in making Belenenses the dominant force in Portuguese football pre-Liga, and the club won three national titles in the 1930s. "Being in a noble part of Lisbon," Pereira said, "tied to voyages of discovery and Portugal's 16th-century expansion, being in the place from where ships left for Brazil and India, gave the image of it being a 'rich' club, and the club made the most of it."

The league title was clinched with a 2-1 win on the season's final day, at Alentejo side SL Elvas, on 26 May 1946 but the balance of power quickly tipped across Lisbon to Sporting, with the golden period of Os Cincos Violinos — 'the Five Violins' — the name given to the attacking quintet of Jesus Correia, José Travassos, Vasques, Albano and the Portuguese league's all-time record scorer, Peyroteo. Yet Belenenses were still able to compete at this point. 

"Just as Benfica had Eusébio and Mário Coluna from Mozambique," said Pereira, "Belenenses had the brothers Matateu and Vicente, two players who made a big impact on Portuguese football." Matateu was the first Luso-African star of the Portuguese game, while Vicente captained Belenenses to a second Taça de Portugal title in 1960 before starring for Portugal in defence at the 1966 World Cup in England. 

On two afternoons per week, you can walk around the trophy room at the Restelo. Two storeys of cups and pennants await behind the barred door. Many of them were awarded for other disciplines — like most clubs in Portugal, Belenenses is a multi-sport club — including swimming, rugby and handball. When I visited, the club historian and museum curator Ana Linheiro proudly pointed to a black and white photograph of herself on the wall, taken around the time of her 1944 and 1945 national swimming titles. 

The museum is full of reminders of the extremely well-connected history of the club. One pennant, from Real Madrid, commemorates Belenenses's December 1947 visit to play the Spanish side on the occasion of inaugurating the Estadio Santiago Bernabéu (or the Estadio Real Madrid Club de Fútbol, as it was then). The view from the upper floor, through battered windows out into the stadium and towards the glistening Tejo and Belém's central strip, reminds you where you are. Yet the club itself appears trapped in there, suffocated by its illustrious past.

"Today, it's exactly this location that is preventing the club having financial sustainability," Pereira said. "They can't build a new stadium and they can't build commercial add-ons to lease — and give them a financial return — because of the visual and environmental impact that it would cause, with the Estádio do Restelo being behind the Mosteiro dos Jerónimos [the imposing 1490s monastery which has been a Unesco world heritage site since 1983]."

Belenenses's decline arguably began in the 1960s, when they — along with the rest of the country — were left in Benfica's slipstream, as Eusébio, Coluna and company led Portugal to triumph in Europe. Belenenses were Portugal's first Inter-Cities Fairs Cup entrant, debuting with a 3-3 draw away to Hibernian in September 1961. Unfortunately for the Blues this was pretty much a non-event even at the time, as Bela Guttmann had led Benfica to become the first side other than Real Madrid to win the European Cup, beating Barcelona in Bern, four months earlier.

There were warning signs of the hardship to come in 1981, when it first became clear there were serious financial problems at the club. The inexperienced coach Artur Jorge bore a significant portion of supporters' wrath for the situation and Belenenses were relegated from the top flight for the first time in their history at the end of the season, in May 1982. In the season following relegation, a 19-year-old José Mourinho played for the club. His father, the goalkeeper Félix, had also played for Belenenses in the late sixties and early seventies, finishing runners-up to Benfica in 1973 and later having a brief spell as assistant head coach. 

Belenenses went back up in 1984 and the previous problems were treated as a blip. Or not treated, if you prefer. "Even when Belenenses were earning a lot of money," Pereira said, "they didn't take financial sustainability into account. They won another Taça de Portugal [in 1989] while being coached by [the 1974 Brazil World Cup captain] Marinho Peres, but good sporting results like this and participation in the Uefa Cup hid the club's financial weakness. For this [competition] they had to sign good players but they didn't have the money for it. They borrowed, didn't pay their taxes and today they're suffering for all these mistakes."

Remarkably, Belenenses were in the Uefa Cup as recently as 2007, and welcomed Bayern Munich to the Restelo in October of that year in the first round, eventually losing 3-0 on aggregate. Again, the headline disguised the reality of the club's situation. Belenenses should have been relegated in 2006, but were reprieved when an administrative dispute between the Liga Portuguesa de Futebol Profissional (LPFP) and Gil Vicente saw the northerners sent down in their stead. They later had a similar escape, in 2009, finishing second-bottom but let off when the financially stricken Estrela went in their place. Moreover, just 7,000 had attended the game with Bayern at the 20,500-capacity Restelo. 

Today, that would be considered a bumper crowd. In their last season in the top flight — 2009-10 — the 15 Liga games at the Restelo produced an aggregate attendance of 50,658. Last season's average in the second tier was 1,396. "At this moment, there are no investors with the capacity or the will to put in the €10m-plus to make the club viable," Pereira said. "After the death of president Cabral Ferreira [in 2008] there was the chance of the Brazilian company Traffic Sport investing, but the then-president Fernando Sequeira rejected the proposal, and this proved to be a big mistake." 

These errors keep stacking up. A recent partnership agreement signed with AC Milan gives the Italian giants access to the club's academy products but — bizarrely — doesn't require them to pay any compensation for any players they decide to take on. Losing out on valuable talent is nothing new for Belenenses. "Bebé was training at Belenenses," Pereira said. "The club didn't want to commit to signing him to a contract, so he went to Guimarães instead and they sold him to United for €8m. A decade before, the same thing happened with Pedro Pauleta." Those who don't slip through the net can expect wages to arrive late. 

While the roots of Belenenses' status lie deep in the past, the rise of Boavista to surpass them as Portugal's fourth most-decorated club is a more modern phenomenon. Despite now playing in the suburbs of Porto, Boavista were born on the banks of the river Douro, where the port wine lodges that give the city its fame reside. 

The club was formed in 1903 as the Boavista Footballers by workers from the Graham distillery and initially run by a six-man board, made up of three English representatives and three Portuguese. A schism quickly developed and a dispute arose in 1905 with the church-going English wanting games played on Saturday and the Portuguese keen to switch to Sundays. A general assembly vote in April 1909 came down on the side of the Portuguese.

The rights to the Campo do Bessa — the site on which a full stadium, Estádio do Bessa, was later built — were also ceded to the victors and the ground was officially inaugurated under that name in April 1910, with a game against the local side Leixões. In that year, the Boavista Footballers became Boavista Futebol Clube. 

This workers' team thus began a respectable history, albeit one hardly laden with trophies. Until 1975's Taça de Portugal win, the highlight had been winning the second-tier title (then, pre-Liga de Honra, the Segunda Divisão) in 1937. The club's first silverware had come with the ten-team Campeonato do Porto in 1914, on 28 June — the same day that Archduke Franz Ferdinand was assassinated in Sarajevo. 

Things began to change under the reign of Valentim Loureiro, a former army major who was Boavista president for a marathon term stretching from 1972 to 1995. He also served as LPFP president for 10 years from 1996. Valentim's son João succeeded him at the Bessa in 1997 and presided over a decade of unprecedented success which took in the Liga title in 2001, another Taça de Portugal, a Supertaça de Portugal (played out between Liga and Taça winners) and three Champions League qualifications. 

To say Loureiro the elder has had his finger in a few pies is something of an understatement. Latterly a local politician, he was also chairman of the ostensibly impressive but disastrously loss-making Porto Metro. Opened in 2002, the total cost of the light railway in Portugal's second city had risen to almost €3.5bn by 2007, having made a record €120m annual loss in 2006. Nevertheless, the board still paid itself a total of €650m in that year. A new line, the metro's sixth, opened in January 2011. Debts mounted to over €2bn. 

"Valentim Loureiro was for Boavista what Geppetto was for Pinocchio," wrote Manuel Dias in his 2001 book O Futebol no Porto. "If the old carpenter saw his wooden doll transformed into a boy of flesh and bone, this tenacious leader made from a club of small dimensions and limited ambitions one of sporting power on a national scale… and he didn't even need the help of a fairy godmother."

Nowadays, the oil in the magic lamp has run dry. Boavista would be grateful for Belenenses's league placing at least, languishing as they are in the modern day Segunda Divisão; the regionalised third tier, where their local rivals are Gondomar, the satellite town which Valentim still serves as Mayor. The stadium there holds fewer than 2,500. 

The shock with Boavista is that they always seemed so well run, among a field of basket cases. Throughout the nineties the club appeared to be balancing the books with what was almost a cottage industry in moving players on to Benfica, notably Nuno Gomes and João Vieira Pinto. Again, the sheen of success — and, in this case, regeneration — concealed what was going on behind the scenes. 

Of course, winning a title in 2001 is light years away from the experience of doing so in the nascent professionalism of 1946. For a club of Boavista's size, it is almost equally a curse as it is a blessing. Success necessitates big bonuses, improved contracts and high overheads for the scale of 'production' required for Champions League matches. A plethora of demands, in short, that the club's infrastructure was ill-equipped to cope with. 

What really did for Boavista was the Apito Dourado [Golden Whistle] enquiry and the subsequent Apito Final [Final Whistle] investigation, both centred around accusations of match-fixing via influencing officials. In the former enquiry, which began in 2004 and concluded in 2008, Valentim was found not guilty of corruption, but guilty of "abuse of power" and given a suspended jail sentence of three years and two months. 

Apito Final had dire consequences for Boavista, above and beyond besmirching of individual reputations. In May 2008 the club was relegated for "coercion" of match officials in three Liga games, against Belenenses, Benfica and Académica. João Loureiro was suspended from office for four years. In the same enquiry, the champions and city neighbours Porto were docked six points for attempted (but crucially, not successful) bribery — a penalty which didn't affect their comfortable Liga title win. The Porto president Jorge Nuno Pinto da Costa was banned for two years in the same judgement.

This ruling was upheld by the Federação Portuguesa de Futebol (FPF)'s Conselho da Justiça [Justice Council] two months later, despite neither the president nor vice-president of the council attending the hearing. The irregularity in this panel's conduct saw both Pinto da Costa's ban and Porto's points penalty revoked by a Portuguese administrative court in 2011. 

Despite this and the fact that Porto's criminal judges absolved Loureiros, the referee Jacinto Paixão and the referees' chief Pinto Correia in July 2010 of the charges brought in Apito Dourado regarding the Boavista v Estrela match in April 2004, Boavista are still waiting for their own recompense. "We continue to believe that the truth will come out," said the club president Álvaro Braga Júnior in a press conference that followed the failed appeal. Boavista have kept believing, but it has done little good. In April 2009, supporters marched the 4km up the Avenida da Boavista to the Câmara do Porto [city hall] to protest, with Justiça Para O Boavistaas their slogan, which was reprised in a May 2011 march and is regularly seen on a banner which follows Portugal's national team around Europe. 

Before the march Braga Júnior told Jornal de Notícias that "the city has already lost Salgueiros but, now, can't afford to lose Boavista, which has 105 [sic] years of history." Salgueiros went to the wall in May 2005, but a phoenix club, Sport Clube Salgueiros 08, was formed three years later. 

Braga Júnior was in no way exaggerating the extent of Boavista's inability to cope with the sanction. After a disastrous 2008-09 season they fell straight through the second tier, but seemed to be granted a reprieve when Vizela were demoted for corruption. In July 2009, the LPFP's executive committee withdrew the offer and demoted Boavista to the Segunda Divisão after they failed to deliver the €150,000 required in financial guarantees, despite the board claiming in a statement they were "just a step away from providing them". 

Boavista are still there, battling for promotion in front of crowds in their hundreds at the Bessa. The old stadium retains a strong sense of its English roots, with the stands close to the pitch, but it feels like a long time since matches were played in front of full houses here during Euro 2004. 

There was little drip-down from those three heady weeks. A 2010 report by TVI noted that Boavista earned just €1.01m in rights from Euro 2004; a figure that appears even more paltry when compared to the harvest reaped by os três grandes: €79m for Benfica, €94m for Sporting and a staggering €133m for Porto. 

Without having had much of a tangible benefit from the Euro 2004 bump, the club is still lumbered with its share of costs. Boavista spend €11,000 per month just to light the Bessa. At the current rate, it takes seven home games to make enough money to cover it. 

Last year brought the tenth anniversary of Boavista's title triumph, though the party was understandably a muted affair. A low-key lunch was organised in Porto city centre in May 2011, with Martelinho, Rui Bento and the former Portugal goalkeeper Ricardo among the attendees from the championship-winning side. In a further attempt to drum up enthusiasm via nostalgia, the club produced a promotional video for this season. 

It was filmed at the Bessa, and included interviews with past greats including Ion Timofte, Nelo and the title-winning midfielder Petit. Its title was "Eu acredito" [I Believe] with all the protagonists and various fans reciting the phrase to camera to conclude the film, affirming their faith in Boavista's ability to bounce back. If they had the grace to participate, most of the players involved also had the realism to look a bit sheepish while they were saying it. 

There is little option but to keep on trying. It seemed as if a breakthrough had been made on February 28, when the Tribunal Administrativo e Fiscal de Lisboa ruled the decision by the CJ's skeleton board null and void. An emotional Braga Júnior greeted the decision and called for the "swift reintegration" of Boavista into the top flight. They're still waiting.

Manuel Maio replaced the weary Braga Júnior as president in June, and he hopes to right the enduring wrongs with fresh energy. "We will only beat our difficulties and be able to have the security we need," he told the club's website, "via the club being returned to its due sporting place which the club's by right – in the first division of Portuguese football."

Boavista, and Belenenses, are swimming against the tide in the current Portuguese climate and have begun to look like relics from a bygone era. Ana Linheiro looks after the Belenenses trophy room on her own, dusting the trophies and neatly collating the daily sports press in arch lever files, as she has done for years. "I used to have someone who helped me to polish the trophies," she says, "but the club had to let her go at the end of last season. The club has no money. What can you do?"

When Estrela Amadora finally folded, it took a week for the administrator Paulo Sá Cardoso to announce to the world that the club was no more. Despite their places in history, both Belenenses and Boavista are local concerns too, so while they will continue to be represented as a dogged minority, the rest of Portugal will turn a blind eye, with even football fans still offended by the public expenditure on white elephant stadiums for Euro 2004 and unlikely to be clamouring for a bailout. As Portugal stares into a gaping economic black hole, it seems that many of its public have decided that some things are simply more important than football.