In Manteigaria Silva, one of Lisbon’s oldest delis, not much has changed since 1928. Cured hams dangle from the ceiling, port and Madeira wines compete for shelf space and slabs of golden cheese await the blade. And alongside the lombo (air-cured pork) and chouriço (chorizo) lies a sausage so thoroughly Portuguese that a 2011 public vote declared it one of the nation’s seven gastronomic wonders: alheira.

Alheira likely saved hundreds, maybe thousands, of souls

In countries that eat sausages, a high proportion of filler is not generally considered a positive. But in Portugal, alheira, a garlicky affair stodgy with breadcrumbs, is highly prized. And it’s much more than just comfort food. In a time when Jews were being persecuted in Rossio Square, just metres from where Manteigaria Silva’s cream awning extends today, alheira likely saved hundreds, maybe thousands, of souls.

Every dish can tell a million stories, if only there’s someone to hear them. Yet Portugal’s cuisine is more narrative-heavy than most, a complex tapestry of invasions and colonisations that slips and slides between continents and religions.

You may also be interested in:

• The ugly story behind a breakfast meat

• The dessert that’s blocked at borders

• Why you can’t get ‘Jewish food’ in Israel

“Like many dishes in Portugal, the most popular and time-honoured ones have stayed with us over many centuries from the period of Moorish rule – also known as a golden era for Jews in Western Europe,” Paolo Scheffer, an expert on Lisbon’s Jewish history, explained.

From the 8th Century, the sophisticated Muslim culture from North Africa that outsiders called the Moors ruled much of Iberia, including the hilly city known as Al-Ushbuna. A Jewish community had long lived and flourished here, and Jews and Muslims lived in harmony.

Jews and Muslims both left their gastronomic mark on modern-day Lisbon

From marzipan and rosewater pastries to soups, stews and sausages, citizens of both religions left their gastronomic mark on what is today the city of Lisbon. “We have Moorish sausage, Moorish fish dishes and even Moorish broth, which is now a seafood dish called cataplana,” Scheffer observed. “But those dishes would have adhered to Judaic and Islamic dietary laws without the popular ingredients added today like shellfish, pork and rabbit.”

By the 12th Century, when Christian crusaders first roared through Lisbon, raping and murdering Muslims, Jews and fellow Christians alike, the city already had its own culinary culture: Christian elements, such as pork and shellfish, merged with this established set of flavours. Later, as Portuguese navigators spread across the globe, ingredients like tomato, chilli and black pepper would leave their mark in turn. At times, Scheffer said, it’s hard to separate what’s now identified as Christian Portuguese food from the established Arab and Jewish cuisines.

Following the tradition set by the Moors, medieval Portugal, even after the Christian conquest, was a generally tolerant place. However, in 1492, Ferdinand of Aragon and his warrior queen Isabella of Castile defeated the last Moorish emirate – Granada – and took the Alhambra Palace as their own.

Avid Catholics, Ferdinand and Isabella believed that practising Jews might encourage those who had converted to Christianity to go back to their old religion. They appointed interrogators to persecute the Jews in their kingdom: their rule of terror would be known as the Spanish Inquisition.

As a result, tens of thousands of Jews who had flourished in Moorish Al-Andalus were thrown out of Spain. They fled to Portugal, particularly Lisbon, but the city did not stay safe for long. After overcrowding caused a plague outbreak, Christian citizens forced all Jews to live outside the city walls.

By 1496, Portugal’s Jews were also forced to convert to Christianity, or leave. Ten years later, rampaging citizens and sailors killed thousands of converted Jews in a citywide pogrom. In 1536, the Inquisition formally arrived in Portugal, and soon both practising Jews and Jews who had converted to Christianity were among the unfortunates parading in penance or burnt at the pyre in Rossio Square.

Jews went to huge lengths to conceal their faith

Disguising themselves as Christian converts, Portugal’s secret Jews went to huge lengths to conceal their religion – from writing Hebrew prayers in Catholic prayer books to combining Jewish words with Catholic rituals. (One community in Belmonte kept its faith alive in secret for more than 400 years.) In the rugged mountains of northern Portugal’s Trás-os-Montes, one of these hidden communities created Portugal’s best-known alheira sausage: Alheira de Mirandela.

In Trás-os-Montes every home preserved pork sausages to see the family through the winter, hanging them from the rafters in meaty coils. Jews – who did not eat pork – were conspicuous for their missing sausages.

“They were seeking refuge from the Inquisition,” Scheffer explained. “So the town of Mirandela developed a bread sausage that could fool informers and local zealots who denounced them to the Inquisition for not eating pork.”

To Ashkenazi Jews, Scheffer observed, the Alheira de Mirandela seems very like kishke, a kosher sausage stuffed with fat, meal and flavourings that’s often served in the slow-cooked Jewish Sabbath bean stew known as cholent. The Jews of Trás-os-Montes traditionally made theirs with bread and chicken, although a present-day Alheira de Mirandela is no longer kosher and can include everything from pork to game, or even be vegetarian.

Today, the alheira has travelled far beyond the mountains. Rather like the British banger, it’s a comfort-food staple. It’s ubiquitous in supermarkets and appears alongside steak and eggs in workers’ cafes or neighbourhood diners.

At Zé dos Cornos, a white-tiled little place below Lisbon’s Castelo de São Jorge, I watched local workers chow down from huge rectangular plates. The Alheira de Mirandela came glossy, grilled and horseshoe-shaped, alongside a fried egg, French fries and white rice. In the smoky and garlicky sausage, chunks of juicy game mingled with chunks of sour, soggy breadcrumbs.

The Moors, most of whom, despite their North African ancestry, had known no home but Al-Andalus, stayed in Lisbon for a long time. Even today, the hillside district where they lived is known as Mouraria (Moorsville). But it was not until the early 19th Century that Jews began to return and, even as Hitler rose to power, there were no more than 1,000 Jews in Lisbon.

Yet, during the early days of World War II, the neutral city again became a refuge for Europe’s Jews. Defying the dictator Salazar, Portuguese diplomat Aristides de Sousa Mendes issued travel documents to thousands of Jews: more than 10,000 Jews would set sail from Lisbon to safety across the Atlantic.

Today, although towns and cities across Portugal are beginning to rediscover their Jewish history, the alheira is more a part of mainstream Portuguese cooking than a symbol of the people who created it. Like the Portuguese word for ‘Saturday’ – 'Sábado', for the Jewish Sabbath – and the brilliant Arab-influenced tiles that illuminate Lisbon's teetering streets, the sausage is an indicator of a past as cosmopolitan as it is complex.

Culinary Roots is a series from BBC Travel connecting to the rare and local foods woven into a place’s heritage.

Join over three million BBC Travel fans by liking us on Facebook, or follow us on Twitter and Instagram.

If you liked this story, sign up for the weekly bbc.com features newsletter called "If You Only Read 6 Things This Week". A handpicked selection of stories from BBC Future, Earth, Culture, Capital and Travel, delivered to your inbox every Friday.