A Vatican tribunal has convicted a cardinal of embezzlement and sentenced him to five-and-a-half years in prison.

Cardinal Angelo Becciu, the first cardinal prosecuted by the Vatican criminal court, was absolved of several other charges and nine other defendants received a combination of guilty verdicts and acquittals among the nearly 50 charges brought against them during a two-and-a-half-year trial.

Becciu’s lawyer, Fabio Viglione, said he respected the sentence but would appeal against it.

Prosecutor Alessandro Diddi said the outcome “showed we were correct”.

The trial focused on the Vatican secretariat of state’s 350 million euro (£300 million) investment in developing a former Harrod’s warehouse into luxury flats. Prosecutors alleged Vatican monsignors and brokers fleeced the Holy See of tens of millions of euros in fees and commissions and then extorted the Holy See for 15 million euros (£12.9 million) to cede control of the building.

Becciu was accused of embezzlement-related charges in two tangents of the London deal and faced up to seven years in prison.

In the end, he was convicted of embezzlement stemming from the original investment of 200 million euros (£172 million) in a fund that bought into the London property, as well as for his 125,000 euros (£107,000) donation of Vatican money to a charity run by his brother in Sardinia. He was also convicted of using Vatican money to pay an intelligence analyst who in turn was convicted of using the money for herself.

The trial had raised questions about the rule of law in the city state and Francis’s power as absolute monarch, given that he wields supreme legislative, executive and judicial authority and had exercised it in ways the defence says jeopardised a fair trial.

The defence lawyers praised Judge Giuseppe Pignatone’s even-handedness and said they were able to present their arguments fully. But they lamented the Vatican’s outdated procedural norms, gave prosecutors enormous leeway to withhold evidence and otherwise pursue their investigation nearly unimpeded.

Prosecutors had sought prison terms from three to 13 years and damages of over 400 million euros (£343 million) to try to recover the estimated 200 million euros they say the Holy See lost in the bad deals.

In the end, the tribunal acquitted many of the suspects of many of the charges but ordered the confiscation of 166 million euros (£143 million) from them and payment of civil damages to Vatican offices of 200 million euros. One defendant, Becciu’s former secretary Monsignor Mauro Carlino, was acquitted entirely.

The trial was initially seen as a sign of Francis’s financial reforms and willingness to crack down on alleged financial misdeeds in the Vatican. But it had something of a reputational boomerang for the Holy See, with revelations of vendettas, espionage and even ransom payments to Islamic militants.

The secretariat of state, for example, sought damages to fund a marketing campaign to try to repair the reputational harm it says it incurred. Even the Vatican communications department said the trial itself had been a “stress test” for the legal system.

Much of the London case rested on the passage of the property from one London broker to another in late 2018. Prosecutors allege the second broker, Gianluigi Torzi, hoodwinked the Vatican by manoeuvring to secure full control of the building that he relinquished only when the Vatican paid him off with 15 million euros (£12.9 million).

For Vatican prosecutors, that amounted to extortion. For the defence — and a British judge who rejected Vatican requests to seize Torzi’s assets — it was a negotiated exit from a legally binding contract.

In the end, the tribunal convicted Torzi of several charges, including extortion, and sentenced him to six years in prison.

It was not clear where the suspects would serve their time. The Vatican has a jail, but Torzi’s whereabouts were not immediately known.

The original London investigation spawned two other tangents that involved the star defendant, Becciu, once one of Francis’s top advisers and himself considered a papal contender.

Prosecutors accused Becciu of embezzlement for sending 125,000 euros in Vatican money to a Sardinian charity run by his brother. Becciu argued that the local bishop requested the money to build a bakery to employ at-risk youths and that the money remained in the diocesan coffers.

The tribunal acknowledged the charitable ends of the donation but convicted him of embezzlement, given his brother’s role.

Becciu was also accused of paying a Sardinian woman, Cecilia Marogna, for her intelligence services. Prosecutors traced some 575,000 euros (£494,000) in wire transfers from the Vatican to a Slovenian front company owned by Marogna and said she used the money to buy luxury goods and fund vacations.

Becciu said he thought the money was going to pay a British security firm to negotiate the release of Gloria Narvaez, a Colombian nun taken hostage by Islamic militants in Mali in 2017.

He said Francis authorised up to 1 million euros to liberate the nun, an astonishing claim that the Vatican was willing to make ransom payment to al Qaida-linked militants.

The tribunal found both Becciu and Marogna guilty and sentenced Marogna to three years and nine months in prison.