Glorious Stage (2003-2008)
After a lapse of 22 years, and just 3 years after being in the lowest division, Msida St. Joseph made their return to Malta's top division. In what proved to be a very difficult season, Msida St. Joseph managed to remain in the Premier following a win in the final match against Balzan Youths. Although it was a difficult season one cannot forget some memorable results which include the 4-1 win against Sliema, 3-1 win against Valletta and the 0-0 draw against Birkirkara.
Following the first season in the premiership there was a change in the administration of the club. Roberto Goveani formerly of Torino Calcio, became the new president of the club. The expectations were quite high. The team narrowly missed a place in the Championship Pool, but they made up for it in the relegation pool, when the club mathematically safe after just 3 games. Thus this helped the club to focus on the FA Trophy. In one of the most amazing runs, Msida managed to arrive to the final. Led by the brilliant Mario Petrone, the club defied all odds to eliminate Mosta, Senglea, Hibernians and Marsaxlokk. The semifinal against Marsaxlokk will be remembered for all the drama it had. Msida equalised in the last minute of extra time, and then went on to win in the penalty shootout after two great saves by Omar Borg. For the second time in history and the first time in 93 years, Msida St. Joseph were again in the final of the FA Trophy. The Final was a great match. The first half ended 0-0, but then early in the second half, the team suffered a double blow. First Bkara scored and then a minute later Msida were a man down. But despite being with 10 men, Msida managed to equalise through Manuel Boni. But just a minute later Bkara scored again, and that was it. Msida lost the final 2-1.
Following the successful 2004/05 season, there was again a change in administration. Roberto Goveani resigned from President and Dr. Kevin Deguara became the new president, whilst Edward Calleja, Robert Farrugia and Keith Abela-Wadge formed part of the new executive board. The club set a target of getting in the Championship Pool for the first time ever. The first thing was to sign one of the best foreigners to ever grace the Maltese Islands, Olalekan Ibrahim Babatunde. Together with marksman Daniel Nwoke, now in his 4th season with Msida, they made great tandem in attack. In January third foreigner was signed. In Babatunde, Nwoke and now Ousseni Zongo, Msida definitely had the best trio of foreigners in Malta. The three foreigners together with the emergence of the youngsters Tyrone Farrugia, Paul Fenech and Josef Mifsud, helped the team to achieve its target, that of getting to the Championship Pool for the first time ever. It was achieved in the last match of the first phase, in the derby against arch rivals Hamrun Spartans. Msida needed a win at all cost and in an amazing match, Msida managed to win 2-0 to write history yet again. The Championship Pool was something new for Msida, and the majority of the matches were quite difficult but Msida managed to get some amazing results like 0-0 and 1-1 against Hibernians and the 3-3 against Sliema Wanderers.
The following season the team had another change in presidency when Edward Calleja started the season as acting president and then after a couple of months Antoine Portelli became the new president of the Club. During the off season the team strengthened itself with the signings of players like Peter Pullicino, Roderick Baldacchino and Pio Sciriha. Following a good start of the season, the team spent the first half neck to neck with Marsaxlokk FC and made it to the Championship Pool for the second season running. Unfortunately at the end the team ended up in sixth place.
At the beginning of season 2007/08, following Antoine Portelli resignation from President, long term committee member Mr. Robert Farrugia became Club’s President. The Club sold some of its assets but managed to sign one of the most interesting foreigners to ever arrive in Malta, Njongo Lobe Priso Doding. Even though the team ended up in the relegation Pool, the team made sure of salvation early on the season. During the relegation the team managed to get its biggest win ever, against arch rivals Pieta, with the score of 7-0, where Njongo Lobe Priso Doding became the first ever Msida St. Joseph FC to score 5 goals in one match.
The following season the team continued to sell some of its assets, but still competed really well in the first phase where the team was just 1 point away from securing another Championship Pool appearance. Unfortunately the team suffered 3 losses in the last 3 matches, whilst our nearest rivals Marsaxlokk won its three matches and thus the Club ended up in the relegation pool for the second year running. At the end of the first phase, it started to come out that the local police and MFA were investigating a corruption case involving Marsaxlokk’s match against our Club in the first round. The Maltese Courts immediately ruled that there was foul play involved by Marsaxlokk but the MFA didn’t come to a decision. When the relegation pool started, the uncertainty of the Marsaxlokk case was playing on the players’ minds, and the team ended up sharing bottom place with another 2 team. This led to a decider being played between Msida and Tarxien which at the end our team lost on penalties to be relegated. Still as the season came to an end, no one was sure in what division the team would play since the Marsaxlokk case was pending. Finally just weeks before the First Division had to start, and a couple of days after the Premier Division started, Marsaxlokk were found guilty and demoted to the First Division, and our club was re-instated to the Premier Division. Unfortunately with all the uncertainty surrounding our club, the majority of the players had left and the Club ending up fighting a lost cause. Financial problems continued to cripple the Club and at the end of season 2009/10 the team ended in bottom place with a negative amount of points.
After 7 years in the Premier Division the Club prepared for its first experience in the First Division. The committee decided that it was important to focus on the financial aspect and not on the team. This made the team weak and by the end of the season, the team only took 2 draws. One has to remember a fine 3-0 win against league winners Balzan Youths which was overturned by the protest board, where the board never found the Club guilty of anything. Although it was a very difficult season, three important things were achived. First the club started to see the end of the dark tunnel when it comes to financial difficulties, and slowly but surely the club started to get on better financial footing. The second important thing was that due to the financial difficulties a lot of youngsters from the Club’s Nursery started joining the first squad and made their debuts during this season. It was a really good experience for these players for the seasons to come. The third and most important thing that the Club managed to achieve was to sell its old premises, and acquire a lease on a new premises which were going to be converted into the new Club House and Bar in the most central part of Msida, that is exactly side to the Church.