MIGDAL, Israel — For the Rev. Juan M. Solana, it was the spiritual equivalent of striking oil.

When he set out to develop a resort for Christian pilgrims in Galilee, he unearthed a holy site: the presumed hometown of Mary Magdalene and an ancient synagogue where experts say Jesus may well have taught.

The project, which Father Solana, a Roman Catholic priest, describes as “providential,” will be blessed by Pope Francis during his visit to the Holy Land this month.

The story starts in 2004. Father Solana, who directs the Pontifical Institute Notre Dame of Jerusalem Center, a century-old complex that provides accommodations and a serene gathering place for Christian pilgrims, thought of building a similar facility in the Galilee region of northern Israel, where the Bible says most of Jesus’ ministry and miracles took place.

After a search for suitable land, four privately owned plots were acquired on the northwest shore of the Sea of Galilee near the small Israeli town of Migdal and the destroyed Arab village of Al-Majdal. Both were named for the ancient town of Magdala, where the name of Mary Magdalene, one of Jesus’s most faithful followers, suggests she was from.

Father Solana’s plan was to knock down the holiday cabins of the old Hawaii Beach resort, built there in the 1960s, and erect in their place a hotel for 300 guests, a restaurant and a lakeside spirituality center for prayer and contemplation. Architects were hired, and the building permits finally came through in 2009. All that remained before construction could begin in earnest was to carry out a salvage dig on the site, a routine requirement in Israel. The Roman Catholic Church and the archaeologists dispatched by the Israel Antiquities Authority did not expect to find anything significant, and intended to get the dig over with as quickly and cheaply as possible.

But their spades struck history only a little more than a foot below the surface: a stone bench that, it soon became evident, was part of the remains of a synagogue from the first century, one of only seven from the Second Temple period known to exist, and the first to be found in Galilee. A local coin found in a side room of the synagogue was dated from the year 29 — when Jesus is thought to have been alive.

Those involved in the project say it immediately brought to mind a biblical verse, Matthew 4:23: “Jesus went all through Galilee, teaching in its synagogues, preaching the good news of the Kingdom of God, and curing the sicknesses and the ailments of the people.” The site of the dig was only about five miles from Capernaum, a known center of Jesus’ activities.

Soon it was clear that the site was not just near Magdala; this was Magdala. The dig went on to uncover an ancient marketplace and a separate area of rooms with adjacent water pools, presumably used for producing the salty cured fish that Magdala was famous for; a large villa or public building with mosaics, frescoes and three ritual baths; a fishermen’s neighborhood, scattered with ancient hooks and other equipment; and a section of a first-century harbor. The ancient synagogue was discovered at the precise spot where the architects had planned to erect an ecumenical chapel, to the right of the hotel entrance.

The discovery of the ruins meant that the building plans had to be changed to accommodate them, and the restaurant and hotel are still under construction. But the new spirituality center is completed, with a boat-shaped altar that blends with a view of the harbor and the Sea of Galilee. “Jesus used to preach to the crowds from Peter’s boat, so we tried to reproduce that idea here,” said Father Solana, who belongs to the Legionaries of Christ, an order founded in Mexico. “Our plans, with a higher providence, merged very, very strongly.”

The pope is not scheduled to visit Magdala during his three-day trip to the region, which will include stops in Jerusalem, Jordan and Bethlehem. Instead, the tabernacle from the boat altar will be taken to the Notre Dame Center in Jerusalem to receive his blessing. Afterward, on May 28, the site will be officially inaugurated as the Magdala archaeological park, and the adjacent spirituality center will be dedicated in the presence of Israeli government representatives and the Latin Patriarch of Jerusalem, Fouad Twal.

A tract of land next to the site has belonged to another Catholic order, the Franciscans, for decades. Excavations there found some ancient ruins, but nothing of the significance of the first-century ruins of Magdala. The Franciscan property remains private, but Magdala has already been opened to the public.

Two Canadians, Roy Fu and Elsie Chew, toured the ruins on a recent rainy weekday.

“It’s not so deep,” Ms. Chew said. “It’s amazing to me that nobody found this before.”

The ancient synagogue had some unusual features, including an ornately engraved stone block that archaeologists say was probably used as a table for reading the Torah. It is carved with columns and arches, a seven-branched menorah with vessels for wine and oil to each side, a 12-leaf rosette and chariots of fire. The stone appears to be a miniature of the Second Temple in Jerusalem, which was destroyed in the year 70, adorned with symbols also meant to commemorate the First Temple.

“We do not fully understand the power of this stone yet,” said Arfan Najar, an archaeologist and co-manager of the Magdala dig, who first came to the site on behalf of the Israel Antiquities Authority and now works directly with the church. “Whoever did this saw the temple with his own eyes.”

Mr. Najar said that Magdala, a Jewish town believed to have been destroyed by the Romans around the same time as the temple, was an especially important discovery because it is not obscured or overlaid with later construction. Every stone that has been found there was from the first century, he said. “It is the window we were missing,” he said, “Jesus in the Galilee.”

Dina Gorni-Avshalom, the archaeologist who manages the dig on behalf of the Israel Antiquities Authority, said the synagogue and the reading table provided researchers with extraordinary insight into the nature of the link between the Jews of the north and the temple in Jerusalem, as well as the connection between Judaism and early Christianity. On top of that, she said, there was sufficient “circumstantial evidence” to assume that Jesus may have set foot there.

In all, the site of the Magdala Center, as Father Solana’s project is now called, occupies more than 20 acres of land, which cost some $16 million to acquire. Completing the project will bring its cost over $100 million, Father Solana said, and only about a third of the necessary funds have been raised so far. Donors are offered sponsorship of one square meter of archaeological digging ($150) or building construction ($1,000). Two Mexican universities — one secular and one affiliated with the Legionaries of Christ — have joined the dig, and nearly 1,000 volunteers from around the world have taken part.

The domed antechamber of the new spirituality center is dedicated to the women who followed Jesus. Mary Magdalene’s presence was prominent at two crucial points in the story of Jesus, the crucifixion and the resurrection; over the centuries, she has been conflated with other biblical women and has come to be associated with the figure of a repentant prostitute and a symbol of redemption.

Here, in a side chapel dedicated to her memory, she is depicted in a large mosaic as Jesus casts out seven demons from her body, with the ancient town of Magdala behind her, an artist’s portrayal based on how the place looks today.