Early on in the six-course, fixed-price dinner at the reimagined Michael Mina, the suited waiter opened a square box like a treasure chest, revealing a dozen containers heaped with spices that seductively assaulted the nostrils. There were pink peppercorn berries, bright yellow saffron powder, fermented lime as black as fertile soil, and other spice blends that looked like a desert sunset.

It becomes the most obvious indication that the restaurant on California Street is charting a new four-star course, as trend-setting as when Aqua opened there in 1991 with Mina as chef de cuisine under George Morrone. In 2002, Mina left to open the original Michael Mina in the St. Francis Hotel. In 2010, he bought Aqua and moved his eponymous restaurant to this space.

From the first bites of a trio of tiny vegetable preparations sprinkled table side with Mina’s spice blends of sumac, urfa and sesame to the stylized basbousa made with coconut, corn and rosewater at dessert, these exotically fragrant flavors are at the core of the experience. Throughout the night waiters sprinkle different mixtures on various dishes to drive that point home.

Coconut-corn basbousa with sweet corn and blackberry at Michael Mina.

Photo: Lea Suzuki / The Chronicle

Then, when diners leave, they get a small vial of spices and a gray envelope that I assumed was the menu, but turned out to be a description of the 19 spice blends used throughout the evening.

After decades of producing exceptional Western food, Mina is following the path of other chefs who are tapping into their heritage for inspiration. It’s quite a change. For years Mina, who now owns 44 restaurants and counting, never publicized his Egyptian roots.

Mina left Egypt when he was 2 years old, and his mother, who is from Cairo, and his father, who is from Alexandria, relocated to Ellensburg, a small town in Washington state. Before long seven of his mother’s nine brothers and sisters ended up in the area, and family celebrations always revolved around their native food.

Mina says he remembers going to friends’ houses and having things like pizza. But when Mina brought the friends home, they would be served unfamiliar food.

Michael Mina at his flagship restaurant, Michael Mina.

Photo: Lea Suzuki / The Chronicle

Like many chefs of his generation, he turned his back on his heritage and pursued Western techniques and cuisines. Through the years he’d experiment with different spice blends at restaurants, such as Sea Blue in Las Vegas. When chef de cuisine Raj Dixit, who is Indian, came into the Mina fold a few years ago, the use of these spices became more pronounced.

A few months ago, Mina and Dixit took the plunge to re-envision the restaurant, featuring only a six-course menu for $155 at dinner, and an a la carte menu at lunch that features a truncated fixed-price option.

The interior looks much the same, although they took out a couple of tables to make the room feel even more spacious, and the service continues to be some of the best in the Bay Area.

However, the food has transformed the experience, making the restaurant even more exciting and relevant. The dinner menu features several selections in each of the six categories. In addition, the chef always sends out a few surprises before the first course arrives and after you think everything is wrapped up.

European turbot with cauliflower, husk cherry, chanterelle and preserved lemon at Michael Mina.

Photo: Lea Suzuki / The Chronicle

The presentations are as manicured as you’d expect given the service and ambience, but looks are deceiving. Each bite features an exploration of spices that beautifully supports the fresh, carefully selected ingredients. The flavor palette sets this restaurant apart from other fine-dining establishments.

The first course on one visit, for example, featured raw chunks of Half Moon Bay prawns arranged to look like a wreath with Early Girl tomatoes, cucumbers, and tiny mustard and radish flowers. The waiter pours harissa broth fragrant with cumin and coriander onto the white mosaic-like plate. On another visit the chef capitalized on the season by stacking a thick slice of tomato, lightly cured in salt, on a similarly sized phyllo pastry draped in brown butter vinaigrette flavored with ducca, a blend of coriander, cumin, mint, thyme and sesame. It’s then topped with slices of black truffles.

While the Middle East might not be associated with some ingredients that dominate the menu, they are tied together with the spices. I’m not sure that you’d get a puffy flatbread topped with a mound of shaved black truffles as part of the bread service, for instance, or hand-cut pasta strewn with caviar. The pasta is blended with kefir, a fermented milk, and rose mallow, a type of hibiscus mixed with galangal, star anise and cayenne.

Mina has always been known for his foie gras presentations, and it’s no different here. Glazed Egyptian mango, poached in spices and caramelized, rests on top of a seared lobe of foie gras on a salty sesame cracker with candied ginger and Mina’s proprietary spice blend. It’s one of the best preparations of foie gras I’ve had, made even more memorable by the wine it was paired with: Les Jardins de Babylone, with a complex sweetness and acidity that further enhanced the food.

Wine pairings done by Jeremy Shanker and Raj Parr cost $130 and consist of seven or eight selections that include some unexpected offerings and elegant reds such as the 2005 Sylvie Esmonin Gevrey-Chambertin Premier Cru Clos Saint-Jacques, which highlighted the cherry component in a squab preparation accented with foie gras.

Some may question using foie gras not realizing that many attribute its invention to Egypt, where you’ll discover hieroglyphics on the walls of the pyramids of ducks being force fed.

It turns out every dish in the second course is memorable: charcoal grilled octopus atop artichokes, creamy saffron potatoes and a hot sauce accented with coriander. There is also a twice-cooked and smoked fairy-tale eggplant stuffed with lentils and surrounded by tangerine-scented yogurt, tomato conserva and a chicken oyster wrapped in a grape leaf.

Rustic flavors and preparations are refined by a plethora of sophisticated techniques. Mediterranean sea bass is set in a green puree of molokhiya, tart green leaves balanced with lobster stock and flavors such as coriander, cumin and Fresno chiles. It’s served next to rings of squid stuffed with a spot prawn mousse.

Mina spent six weeks in his mother’s kitchens to learn her secrets and to reproduce dishes he remembers from his childhood, such as the marble-size falafel that’s served before the first course. Instead of lentils, hers are made with fava beans.

Egyptian macaroni of wild mushroom, bechamel and nutmeg at Michael Mina.

Photo: Lea Suzuki / The Chronicle

Then there’s the macaroni gratin that shows up as a third-course option. At the restaurant, the chefs individually place the macaroni in a terrine glazed with bechamel. It’s then pressed, unmolded, browned and cut into little squares with a bottom that resembles honeycomb. The dish is traditionally served with beef but Mina and Dixit use wild mushrooms and whip the bechamel into a foam as a platform for the macaroni.

The main courses are all boldly realized whether spiced squab with huckleberries, a Yemenite-style rib eye or charcoal grilled lamb with black harissa.

At dessert, pastry chef Joshua Gaulin also riffs on Middle Eastern flavors, especially in the basbousa, a traditional semolina dessert cake he makes with summer corn, coconut and a rosewater simple syrup. However, most items still feel Western, especially the bouchons and chocolates that come with the check. They are something like you’d find in the best chocolate shops in Paris.

I was totally enthralled with the new direction but waited several months to make a final visit to see how the menu had evolved. While the core items remained much the same, some dishes and accompaniments had changed with the season. The execution seemed even more confident than it did on earlier visits, showing that like a good wine, the menu will no doubt get better with age.

It’s clear that Mina and Dixit are at the beginning of their journey and that there’s an even more interesting road ahead as they delve deeper into the cuisine and utilize their immense talents and creativity to bring the flavors of the Middle East to life in a fine-dining context.

Michael Bauer is The San Francisco Chronicle restaurant critic and editor at large. Email: mbauer@sfchronicle.com Twitter: @michaelbauer1 Instagram: @michaelbauer1