They first had to dig through thick concrete, laid down ahead of plans to turn the convent into an army barracks.
But they quickly struck gold, finding a crypt they believe to have been Lisa's final resting place and soon after they unearthed a female-sized human skull.
The skull was found five feet under the convent's original floor along with other fragments of human ribs and vertebrae.
Plans to continue the dig were suspended when the team ran out of funds, but they were able to resume last month.
And this week, they found a human skeleton.
The bones will undergo tests to establish if they match the skull found last year.
Scientists will then compare the DNA in the bones with the remains of the model's two children who were buried nearby in an attempt to authenticate the remains.
Once they have verified the skeleton and skull belong to the modelf orensic artists will attempt to reconstruct her face to see how it compares to the 500-year-old version painted by da Vinci - and perhaps solve the riddle of the Mona Lisa's enigmatic smile in the process.
Archeologist Silvano Vinceti, who is in charge of the dig, explained: 'We don't know yet if the bones belong to one single skeleton or more than one.
"But this confirms our hypothesis that in St.Ursula convent there are still human bones and we cannot exclude that among them there are bones belonging to Lisa Gherardini."
The initial discovery - made using ground penetrating radar and ancient maps and documents - came after a foot of modern concrete was removed and unearthed a layer of ancient, 90-centimeter wide bricks.
Professor Vinceti said of the first discovery: 'This is a very exciting development and the find is consistent with our records and our preliminary research.
"The crypt we have found is the one that was mentioned in church records from 1495 and was reached via a grate and then a staircase.
"We also know from those records that in 1625 there was a second crypt and these are the ones we have found."
Present on the dig is Natalia Gucciardini Strozzi, who is related to Lisa Gherardini and who is also a close friend of Prince Charles and former Prime Minister Tony Blair.
Speaking after the skull was discovered, she said: 'It was so emotional being here - I didn't think I would get so emotional. I am certain that this is the final resting place of Lisa Gherardini.
It is not the first time that Professor Vinceti has used such techniques in his work - last year similar methods were used to locate and identify the remains of Caravaggio, another Renaissance master.
Last year in a Dan Brown-style mystery professor Vincenti also claimed that a hidden message could be seen in the eyes of the Mona Lisa after examining them with a high powered magnifying glass.
The Mona Lisa is an oil on panel painting owned by the French government and the image is so widely recognised and caricatured that it is considered the most famous painting in the world.
Da Vinci started to paint it in 1503 or 1504 and finished it in 1519, shortly before his death, and after he had moved to France.
- DAILY MAIL
