Hiroyasu Kayama’s atmospheric, candle-lit ninth-floor hideaway is one of Tokyo’s most compelling bars, with shelves crammed with rare spirits and jars of obscure aromatics, and drinks just as likely to involve a mortar and pestle as a cocktail shaker. Sink into one of the half-dozen armchairs at the ancient-wood counter and give Kayama carte blanche to work his mixologist magic. Best to get there early, though: Bar Benfiddich’s fame already extends far beyond the Shinjuku back streets. [$$$]

Chef Kotaro Hayashi’s brilliant little hole in the wall is hard to find and even harder to get into. Regulars book weeks ahead for seats in front of the open kitchen where Hayashi puts together inventive, satisfying takes on classic izakaya dishes, pairing them with some of the best small-batch sake from around the country. Don’t miss his signature potato salad, which he tops with half a lightly smoked soft-boiled egg and mustard vinaigrette. [$$]

There’s no shortage of soba specialists in Tokyo, but few manage to create noodles quite as flavorful and satisfying as those at Tamawarai. Each batch is made from scratch — the dough mixed, rolled, and cut by hand — and much of it with buckwheat the restaurant helps to grow. The side dishes, such as soba miso and the wonderfully creamy yuba (tofu skin) are prepared with equal care. It does not accept reservations, so despite the less-than-convenient location in a residential neighborhood between Shibuya and Harajuku, you will invariably find yourself standing in line for up to an hour to get in. [$]

Chef Zaiyu Hasegawa’s decision to move Den from its iconic Jimbocho address has paid off in spades. Two years on and his star is still rising — both with Michelin (Den now has two of them again) and on the Asia’s 20 Best Restaurant list (up to second place). His cooking remains innovative and satisfying, overlaying the principles of kaiseki, Japan’s traditional and often highly formalized cuisine, with ideas and influences that are audacious and humorous. Expect foie gras in your appetizer and ants in your salad, along with his signature “Dentucky Fried Chicken.” [$$$]

Melding flair, precision, and premium local ingredients, chef Hiroyasu Kawate’s intricate 11-course tasting menu (six courses at lunch) is as bold and theatrical as his dining room, a 16-seat counter around a huge open kitchen. The former Quintessence sous chef moved into new premises in early 2015 and is now delivering some of the most exciting, innovative modern French cuisine in the city. [$$$]

Tonki is spartan, spacious, and spotlessly clean, and has been serving tonkatsu the same way since 1939. There’s only one choice to make: rosu (fatty) or hire (lean). Either way, it takes 20 minutes to cook, and is served with shredded cabbage and mustard, with rice and soup on the side. There’s no dessert or coffee. You just wait, eat, and then leave. Classic. [$]

Torishiki takes the basics of yakitori — morsels of chicken that are skewered, grilled, and basted — and elevates them to another level. Owner Yoshiteru Ikegawa uses virtually every part of his premium shamo gamecocks, tending the skewers over his glowing charcoal grill with artisan intensity. Among his specialties: chochin, the rich yolk of an unhatched egg; grilled tofu, rich with chicken fat; and the warming, nourishing chicken broth that closes every meal. [$$$]

There’s a renewed enthusiasm for sake in Japan, based around small-batch, limited-edition regional brews with intense flavors and unique characteristics. Gem by Moto is the place where many of the new generation of enthusiasts gather to enjoy these innovative styles. Manager Marie Chiba knows all the best young brewers — they are responsible for the graffiti covering her walls  — and she has her own cellar where she matures the sake they make especially for her. Another major draw is her extensive and creative food menu. Gem may be a bit off the beaten path, but reservations are essential. [$$]

Nowhere in Tokyo serves tonkatsu (breaded deep-fried pork) with the quality and sophistication of Butagumi. In a 60-year-old, two-story, freestanding traditional house, you dine on premium cutlets — choose from a couple dozen regional heirloom breeds — cooked a beautiful golden brown and served with a pyramid of finely slivered cabbage and thick, homemade Worcestershire-style sauce. [$$]

Yoshihiro Narisawa’s fusion of French haute cuisine — he worked under three greats: Bocuse, Giradet, and Robuchon — with a profound understanding of Japanese ingredients has resulted in a style uniquely his own. Serving brilliant left-field dishes such as Soil Soup (yes, really) and Okinawan sea snake broth alongside superb langoustine and wagyu beef, he more than merits his two Michelin stars and his status on the World’s 50 Best Restaurants list as “Best in Asia.” [$$$$]

“Our passion for ramen makes the town a better place.” Muginae more than lives up to its English-language slogan. Everything about this modest counter on the southern edge of the city shouts quality: house-made noodles, free-range chicken broth, a blend of artisan soy sauces, and zero chemical flavor enhancements. It all adds up to a superb ramen that more than justifies the train ride out from the center of town and the inevitable lines of up to an hour. [$]

Kaiseki, Japan’s ineffable, hyper-seasonal traditional cuisine, always tastes best in its hometown, Kyoto. This can be attributed to the water, which is softer than in Tokyo. Chef Yoshihiro Murata gets around this by shipping water from the ancient capital to the Akasaka branch of his renowned Kikunoi, to ensure his dashi soup stock is always perfect. In this tranquil, secluded setting, it’s almost possible to imagine you have left the metropolis far behind. At lunchtime, Kikunoi also offers more accessible and affordable lunches served in elaborate obento lunch boxes. [$$$]

Owner Kentaro Nakahara sources the finest wagyu and knows all the best cuts to grill over the charcoal burners set into your table top. Besides his seven-item yakiniku (grilled meat) tasting menu, don’t miss the beef “prosciutto,” the tartare, or his self-styled “legendary” grilled tongue (which must be booked in advance). Yakiniku is always fun but it’s rarely as chic, clean, and smoke-free — both from cigarettes and the grills — as it is here. [$$$]

The former geisha district of Kagurazaka is worth exploring at any time, but especially as evening falls on its atmospheric narrow alleys. And even more so if you’ve booked yourself into Ishikawa for an extended, multi-course kaiseki dinner. Hideki Ishikawa’s impeccable cuisine, superb quality ingredients, and gracious welcome have won him three well-deserved Michelin stars and a host of admirers around the world. [$$$]

Although Kyourakutei first made its name as a soba restaurant with noodles made in the time-honored te-uchi (hand-rolled and cut) tradition, it’s the excellent menu of drinking snacks and side dishes (and sake) that makes the restaurant special. The tempura is great and so are the grilled dishes, and the fish couldn’t be fresher. [$-$$]

Chef Koji Koizumi’s impeccable contemporary kaiseki cuisine ticks all the boxes. It is intensely seasonal, inventive, superbly cooked, and beautifully presented. Better yet, it is served with a refreshing lack of formality. Kohaku is an offshoot of nearby Ishikawa, but it has a own distinct identity that make it every bit as worth your time. Koizumi’s six-seat counter is the place to be if you want to watch him at work. [$$$$]

There are three constants at Maruka: the line outside (often an hour long); the rock music (invariably Jimi Hendrix) playing quietly on the sound system; and the chunky, satisfying udon noodles. Eat them hot in a light, fish-based broth or chilled with a dipping sauce. Either way, order some tempura on the side, maybe the chewy squid tentacles, or the whole batter-fried eggs, and see why these are considered the best Sanuki-style udon east of Kagawa. [$]

Oden is Japan’s favorite wintertime comfort food, an aromatic hotpot of slow-simmered seafood, meat, and vegetables, usually washed down with plenty of sake or beer. Otako has been serving it this way for almost a century and attracts an eclectic clientele, from humble salarymen to Ginza hostesses dolled up in kimonos. Slide open the door, wait for a seat, then take your place at the long counter, watching the chefs at work over the steaming oden pans. At any time of year, Otako is a Tokyo classic. [$$]

High-end ramen is no longer a contradiction in terms, least of all in swish Ginza. Kazami looks as gleaming and spotless as a sushiya, and the noodles are put together with just as much attention to detail. The clear, fragrant broth for the shio and shoyu styles is made with kombu seaweed and five types of dried fish. But the stand-out bowl is the original: sake-kasu “soba” (it’s actually ramen), thickened with rich, warming sake lees. [$$]

Long before third-wave coffee arrived in Tokyo, there was a thriving culture of kissaten, old-school coffee shops, usually cozy and smoke-filled. Most have disappeared, but L’Ambre (founded 1948) shows no sign of fading away. Even though centenarian owner Ichiro Sekiguchi died in 2018, his heirs intend to maintain his devotion to premium coffee beans, some of them aged for decades. A venerable Tokyo treasure. [$]

Tradition meets the 21st century at this striking contemporary cafe designed by renowned architect Kengo Kuma inside the University of Tokyo campus. Sit outside and gaze at the greenery while nibbling on warabimochi jelly, kuzukiri noodles, or other artisan wagashi (Japanese confections), prepared to order and served with coffee from the excellent Sarutahiko roasters. [$]

Akomeya is the place in central Tokyo if you’re looking to buy premium rice, foodstuffs from around Japan, kitchen essentials, and designer tableware. But an even better reason for visiting is the casual in-store canteen, Akomeya Chubo. At lunch it serves simple rice-based set meals before morphing into genteel izakaya mode in the evening with an a la carte menu and a reliable sake selection. [$$]

No one has done as much to give Japan’s green tea culture a boost of relevance as interior designer Shinichi Ogata and his Higashiya wagashi (confectionery) shops. At his flagship store, a tranquil, capacious oasis above the madding crowds of central Ginza, the traditional wabi-sabi tea ceremony aesthetic has been given a contemporary makeover. Settle in for contemplation over premium teas, seasonal desserts (including kakigori ice in summer), and even light multicourse meals. You will emerge fully recharged. [$$]

Soba is the traditional noodle in Tokyo, and nowhere is that heritage preserved better than at Kanda Matsuya. Founded 130 years ago and housed in superb wooden premises, it’s a living legend. There’s a small menu of side dishes to go with sake, but here it’s all about the noodles, which are rolled and cut by hand in-house by the master’s son. [$]

Tsukiji’s famous wholesale market finally made its long-delayed move to the new location in Toyosu. But the Outer Market — the compact warren of narrow, crowded streets known as Jogai — has not gone anywhere. Alongside the sushi counters and ramen shops you will find retail stores selling anything from fresh seafood and katsuobushi (bonito flakes) to traditional knives and ceramics. An essential pilgrimage for anyone with an interest in eating! [$-$$]

Housed in a classic low-rise building in a traditional neighborhood, Imahan is one of Tokyo’s oldest and best loved purveyors of beef cuisine. Shabushabu, sukiyaki, teppanyaki or steak: all are prepared and served with old-school refinement and expertise. Book yourself into one of the private rooms for an extended omakase feast. Just choose what provenance and grade of wagyu you want, then relax and let the kimono-clad waitstaff pamper you. [$$$]

Tokyo’s cognoscenti have long championed Takaaki Sugita as one of the city’s top sushi chefs. Now at work in a sparkling new premises in Nihonbashi, he is at the top of his game and finally starting to get the mainstream attention and respect he deserves. Needless to say, Sushi Sugita has become one of the hardest places to book, so out-of-towners should get their concierges working on it well ahead of time. [$$$]