Pope Francis has beatified John Paul I, the happy and humble pontiff known as “the smiling pope”, whose death after just 33 days as leader of the world’s Roman Catholics gave rise to decades of speculation and rumour.

At a ceremony in St Peter’s Square on Sunday, which marked the last formal step before canonisation, Francis praised John Paul I’s brief but cheerful papacy.

“With a smile, Pope John Paul managed to communicate the goodness of the Lord,” he said during mass.

“How beautiful is a church with a happy, serene and smiling face, that never closes doors, never hardens hearts, never complains or harbours resentment, does not grow angry or impatient, does not look dour or suffer nostalgia for the past.”

Seated under a canopy outside St Peter’s Basilica, Francis led the proceedings, which were punctuated by thunder, lightning and rain, prompting cardinals, bishops, the choir and thousands of rank-and-file faithful to open umbrellas.

Born Albino Luciani on 17 October 1912, in the northern Italian town of Canale d’Agordo, John Paul I went on to become Patriarch of Venice, cardinal and then the head of the Roman Catholic church.

Luciani, who took the name John Paul after being elected pope on 26 August 1978, was found dead in bed at his Vatican apartment on 28 September that year.

Although the Vatican said John Paul died of a heart attack, it gave conflicting versions as to the circumstances in which his body was discovered.

Despite initially claiming he had been found by a priest who served as his secretary, it later acknowledged he had been found dead by one of the nuns who used to bring him his morning coffee.

Given the huge financial scandal developing at the time in Italy involving figures who had links to the Vatican’s bank, suspicions quickly took root in the secular media that John Paul had perhaps been poisoned because he intended to tackle wrongdoing.

Books speculating on the circumstances surrounding his death sold millions of copies.

John Paul’s biographer Christophe Henning said the rumours could be explained by the sudden nature of his death and the “calamitous communication” by the Vatican at the time. The absence of an autopsy to determine the cause of death has also helped fuel speculation.

But Henning told Agence France-Presse he had no doubt that the pontiff had died of natural causes, adding that he had been “in fragile health”.

John Paul’s short papacy was characterised by his simple, direct manner of addressing the faithful – a style markedly different from that of his more formal predecessors.

“Let us pray, in his own words: ‘Lord take me as I am, with my defects, with my shortcomings, but make me become what you want me to be,’” Francis said.

The pope added that John Paul had lived “without compromise” and had also “conquered the temptation” to put himself “at the centre or to seek glory”.

Francis advanced John Paul along the path to sainthood last year after crediting him with interceding in the miraculous healing of a child in 2011.

The Vatican said the curing of the 11-year-old girl, Candela Giarda, took place in Buenos Aires, the birthplace of Francis. Giarda had been suffering from acute brain inflammation, septic shock and other serious medical problems and was said by doctors to be on the verge of death. But a local priest took “the initiative to invoke Pope Luciani”, the Vatican added, and she recovered.

Last week, Giarda, who is now 21, told a press conference that she wanted to attend the ceremony, but wouldn’t be able to because she had broken her foot while working out in the gym.

Agence France-Presse and the Associated Press contributed to this report