And he said, “Let there be lobster enchiladas, and let there be morel tamales.”

And so it came to pass that in 1987, chef Mark Miller opened the doors of Coyote Café. He had come to Santa Fe from a food revolution in Berkeley, California, at Alice Waters’ Chez Panisse and his own Fourth Street Grill. And when he applied his fine-dining creativity to New Mexico classics, he helped to spark a nationwide boom in Southwestern cuisine.

More than three decades and a few chefs later, the heirs to his empire are still churning out dramatic cocktails and artful dishes. Over a couple of recent visits, we were wowed by several dishes, though a hiccup in service and a few missteps in execution stood out.

As the origin story in the 1989 Coyote Café cookbook goes, a trickster coyote stole a flute from a medicine man and played it to entertain his animal friends. His siren song seems to have lured both the current chef and owner — each one has symbiotic ties to the place. Executive chef Eduardo Rodriguez began his career washing dishes at Geronimo in 1997, where he trained under the late Eric DiStefano. After DiStefano became co-owner and executive chef of Coyote Café in 2007, Rodriguez followed his mentor to the new gig. And owner Quinn Stephenson, who began his Coyote bar duties at a tender age more than 20 years ago, continues to direct an innovative list of what he calls “culinary cocktails.”

Last year’s lavish renovation of the headquarters in the former bus depot above Water Street transformed the dining room into a contemporary homage to the restaurant’s vibrant — and formerly very 1990s — Southwestern aesthetic. Now, LED projections of alebrijes (bright Oaxacan folk art sculptures of fantastical creatures) adorn the walls; an enormous Dale Chihuly-esque chandelier suggestive of a chile ristra dominates the center of the room; and open banco seating is upholstered in bright striped turquoise and orange. A mural of Coyote and his friends near the bathroom still suggests a forever-’90s undertone — which continues upstairs from the restaurant with the gangster-animal graffiti that adorns the Coyote Cantina.

On a recent evening, snow swirled to the ground outside as bussers, runners, and servers churned around the packed dining room. Despite the swarm of staff, it took about 10 minutes to receive a proper greeting and get our first orders in. One team member even stopped and lingered just beside our window-side table to stare moonily out at the dreamlike blizzard, thoroughly ignoring us. We expected a restaurant of this caliber to impart a more seamless welcome, especially considering the high prices.

The picturesque view was made sweeter by the lime-salt foam atop Stephenson’s longtime signature cocktail — the Salty Señorita ($14), a standout semi-deconstructed margarita, served up, that stokes the Coyote’s reputation as a cocktail mecca.

A roasted corn soup with green chile and chicken albondigas, blue corn tortilla chips, and poblano foam ($15) recalled the Coyote’s original concept of ambitious spins on local flavors. The portion was generous — the soup earthy and sweet, the meatballs tender and piquant — and the poblano essence atop it all provided a light vegetal kiss. An appetizer of squash blossoms stuffed with lobster and mascarpone ($22) seemed to be a classic Mark Miller move. The luscious lobster paired beautifully with the silky cheese and lacy, crunchy blossoms. But I tasted only cream in the accompanying hoja santa crema, rather than the distinct peppery anise flavor of that Mexican herb.

The concentrated flavor of Tellicherry black pepper seasons the elk tenderloin medallions ($43). An indelible entrée that has spent years on the menu, the mostly monochromatic plate included a mound of black garlic mashed potatoes encircled by a french-fried “potato nest.” The dish was rounded out by glistening snap peas, musky white truffles and trumpet mushrooms, and smoked thick-cut bacon, though the buttery, rich medium-rare meat was unmistakably the main event.

A gorgeous filet of Patagonian sea bass ($42) was superbly cooked, though short on flavor. But we were let down by its accompaniment of a thick potato-and-spinach ravioli (too toothy) and a swab of grapefruit butter, which tasted ... like butter.

Another night, we settled into two bar seats situated directly in front of the kitchen line, just a few feet away from Rodriguez and his crew. This position presented a decidedly showier dining experience, as well as more attentive service. We watched the bartender impressively ignite and smoke a cherry wood branch in an elegant decanter. That smoke seasoned the Gentleman’s Vice ($14), a beguilingly moody Manhattan.

The chile morita prawn appetizer with grit cakes and green chile aioli ($20) takes its direction from Miller, who put a shrimp and corn cake dish on the menu decades ago. Rodriguez’s towering spin on the classic was the star of the evening. The spicy shrimp were topped with slender grapefruit wedges and microgreen sprigs and anchored by crunchy cakes. The work of art was sauced with the mild pale-yellow aioli, the last vestiges of which we sopped with the café’s classic whole-kernel cornbread.

In a newer appetizer of seared pork belly, grilled oyster mushrooms, green apple slaw, blackberry mole, and celery root purée ($18), each element burst with its own essence. Every one married well with the velvety, thick white meat in a harmony of salty, sweet, and earthy flavors.

A cognac and foie gras butter failed to fully season the medium-rare filet mignon entrée ($42). We’d also hoped for more seared-in zest there. It was, like the sea bass, impeccably cooked but ultimately fairly bland. But a duck-leg confit ($33) brought us back to the Coyote’s successful suite of signature flavors. The easily shredded, sweet meat made a meal for two, served with a tangy-sweet yellow-squash mole, caramelized onions and cilantro, griddled house-made tortillas, and calabacitas with corn and chayote squash.

Like most of the appetizers we sampled, desserts are easily shared — and impeccably executed. The tamal bread pudding ($12) is a master class in hybridity, with caramel-sticky pudding and pecans cradled in a husk and paired with subtle sweet-corn ice cream. My pal attacked a banana cream pie ($12) with gusto, digging into crackling caramelized bananas topped with a crusty meringue and vanilla ice cream. As with several other plates, the portions were large enough for two or even three spoon-holders.

In 2014, Mark Miller told Texas Monthly of the ’90s trend in Southwestern cuisine, “There was so much richness and depth, it could have continued to this day. There is great, great Southwestern food that has not been cooked.” Eduardo Rodriguez’s dedicated steerage of the ship Miller built suggests that the very best may be yet to come. ◀