For a rejuvenating start to the day indulge with a Japanese breakfast at Yakumo Saryo. Designed by architect Shinichiro Ogata, the teahouse is a tranquil space offering a morning of peace and mindfulness. The asacha (morning tea) set breakfast includes a variety of teas, porridge, fish, pickles, miso soup, and wagashi (confections) to finish. Reservations are required.

Kozue has some of the best views in the metropolis from the 40th floor of the iconic Park Hyatt Tokyo, a view made famous in Sofia Coppola’s Lost in Translation. Chef Nobuhiro Yoshida sources seafood directly from fishermen, who send him photos or videos of their catch while they’re still out at sea so that selections arrive the same day to the restaurant. Seasonal sashimi is presented over a bowl of crushed ice and wagyu beef hot pot arrives on exquisite tableware. Elevate the meal with a flight of sake from the impressive list.

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 extends far beyond the Shinjuku back streets.

No visit to Tokyo is complete without exploring a depachiku — the food halls found on the basement levels of most department stores. Isetan in Shinjuku can’t be beat for gourmet glamor, with local wagashi (Japanese confections) arranged alongside the patisseries of Sadaharu Aoki, Jean-Paul Hévin, and Pierre Hermé. Have a light meal at the in-house open kitchen or take a bento up to the roof garden.

Chef Zaiyu Hasegawa’s decision to move Den from its iconic Jimbocho address has paid off in spades. The restaurant claims two Michelin stars and the top spot in Asia on the World’s 50 Best Restaurants list. The cooking remains innovative and satisfying, incorporating audacious, humorous ideas into Japan’s highly formalized kaiseki tradition. Expect foie gras in your appetizer and ants in your salad, along with his signature Dentucky Fried Chicken.

The new generation of sake enthusiasts gather at Gem by Moto to enjoy innovative, small-batch, limited-edition regional brews with intense flavors and unique characteristics. Manager Marie Chiba knows all the best young brewers — who are also 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.

It’s no secret Tokyo has some of the best French cuisine outside of France, partly because local chefs study with the world's best, as Shinobu Namae at L’Effervescence did with Michel Bras and Heston Blumenthal. The restaurant has built a strong following with its use of premium produce, innate seasonal sensibility, and clear pride in good service, not to mention its tranquil location. Pro tip: Lunch is an especially good value.

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

Second-generation chef Daisuke Shimazaki serves traditional Edomae sushi at Sushi Yuu, located in a quiet residential area not far from the busy Roppongi district. While some high-end sushiya can feel stiflingly formal, more like a library or a church than a convivial restaurant, chef Shimazaki puts all of his customers at ease (in English, Russian, or Italian, as well as Japanese). The meal starts off with small seasonal bites such as grilled Pacific mackerel and simmered yellowtail before the parade of nigirizushi. Sushi Yuu is particularly famous for tuna, which Shimazaki sources from one of Toyosu Market’s top tuna vendors.

Chef Daisuke Nomura serves modern shojin ryori — vegetarian Buddhist cuisine —  strategically locating his restaurant Sougo in the Roppongi district to appeal to the younger, international crowd who live and work in the neighborhood. The signature dish is sesame tofu, fried or grilled to bring out a silky texture. The menu also includes a myriad of vegetables from land and sea, along with traditional shojin ingredients like fu (wheat gluten) and yuba (soy milk skin). Tip: Diners wanting to learn more about Japanese food can take classes at Tokyo Cook, a cooking school located within the restaurant.

Muginae more than lives up to its English-language slogan: “Our passion for ramen makes the town a better place.” 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 bowl of ramen that more than justifies the train ride out from the center of town and the inevitable wait 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 bento lunches.

An L-shaped counter made from a 500-year-old Mongolian oak tree sets the stage for an omakase flight of craft cocktails at Bar Gen Yamamoto. The eponymous proprietor returned from New York specifically to work with the Japanese palette of ingredients. The drinks, made with spirits and sake, are all low in alcohol to highlight the flavors of seasonal produce, both fruits and vegetables, including items like fava beans or sweetcorn. They’re presented in a variety of eye-catching glassware on trays decorated with flowers or greenery. With only eight seats, this ultra-quiet bar is a place to study the art of imbibing.

The former geisha district of Kagurazaka is worth exploring at any time, but especially as evening falls on the atmospheric narrow alleys. Even more so if you’ve booked yourself into Ishikawa for an extended, multicourse 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 sake, drinking snacks, and side dishes that makes the restaurant special. The tempura and grilled dishes are great, and the fish couldn’t be fresher.

At Tenko, vegetables and seasonal seafood from Tokyo Bay are battered and fried into tempura, a specialty of Tokyo. The restaurant is on the quiet backstreets of Kagurazaka in a former geisha teahouse. Second-generation chef Hitoshi Arai is a master at creating delicate and lacy tempura, serving each one as it comes out of the oil, and it’s worth trying some of the tempura with salt instead of dipping sauce to preserve the crispy covering. Part of the experience is listening to the tempura as it bubbles in the hot oil.

Oniyanma is a casual stand-and-slurp handmade udon noodle shop that opens for breakfast. Purchase a ticket from the vending booth outside, then find a spot along one of the counters inside. The most popular order is bukkake cold noodles with a splash of tsuyu sauce, topped with chicken tempura and chikuwa (grilled fish cake) tempura, along with a handful of chopped green onions. Grated ginger and tenkasu (tempura bits) to garnish the noodles are on the counter for diners to apply as they like. (The vending machine options are entirely in Japanese, so for those who can’t read, the most popular noodles are the first option at the top left corner.)

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.

Sachiko Tsukuda creates her unique wagashi (confections) to be paired with sake. Located in the hipster Yanesen district, the salon has earned a cult following among both wagashi and sake aficionados. Tsukuda’s signature is a modern take on dorayaki; she augments the traditional pancakes, typically stuffed with sweet azuki bean paste, by utilizing seasonal jams such as rhubarb or kumquat. She also incorporates vegetables into some of her sweets, such as jelly cakes made with burdock root or red turnips.

Part of the ritual of riding a shinkansen (bullet train) is enjoying a bento and green tea (or sake if you like), while taking in the view. Located inside of Tokyo Station, Ekibenya Matsuri offers about 170 regional ekiben (“eki” for station and “ben” short for bento box) brought in from throughout Japan, an excellent chance to enjoy a range of regional Japanese flavors. The colorful selection includes rice topped with sashimi, wagyu beef, or yakitori grilled chicken skewers, and there is even a gyutan beef tongue bento that contains a warming device activated by a pull-string, allowing you to enjoy a hot meal on your journey. The shop opens at 5:30 a.m. for anyone catching an early train.

As you explore the tranquil, traditional backstreets of the low-rise Nezu district, Kamachiku makes an ideal stopping point. The restaurant serves premium udon (wheat) noodles, kneaded and cut by hand Osaka-style, in a converted century-old red-brick storehouse overlooking a small garden. If you want to settle in, you’ll find a good selection of sake and side dishes.

No one has done as much to give Japan’s green tea culture a boost 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.

At the Blind Donkey (co-owned by chef Shinichiro Harakawa), Chez Panisse alum chef Jerome Waag serves a seasonal menu based on products sourced directly from organic farmers and purveyors from throughout the country. The options typically fall under bistro cuisine like grilled yellowtail and Hokkaido grass-fed beef. Friendly staff can answer questions about the produce and the natural wine list. The teishoku (set lunch) on Thursdays and Fridays includes a colorful variety of vegetables.

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 — hasn’t gone anywhere. Alongside the sushi counters and ramen shops you’ll find retail stores selling everything from fresh seafood and katsuobushi (bonito flakes) to traditional knives and ceramics.

You’ll find dozens of shops lining this street in the Tsukishima neighborhood all serving monjayaki, a local dish similar to Osaka’s okonomiyaki. The setup at every shop is essentially the same: Diners select fillings such as mentaiko (spicy pollack roe), mochi, and cheese, and cook the monja themselves on a large iron plate set into each table with the help of a tiny spatula. The trick is to spread the mixture out thin and wait for it to crisp up (the staff will gladly show first timers the proper technique). Paired with an icy mug of beer, it’s a fun meal. The street is blocked off at night for pedestrians, giving it a lively atmosphere that attracts local Japanese as well as tourists. It’s best to peruse the shops and pop into the first one that seems warm and welcoming.

From your place at the nine-seat wooden counter, watch as veteran master Tetsuya Saotome prepares perfect pieces of tempura. Every bite of seafood or vegetable is served direct from the deep-frying wok to your plate. The matsutake pine mushrooms in autumn are especially memorable. The location is obscure but well worth the taxi fare.

Tokyo’s oldest onigiri shop, Yadoroku, dates back to 1954 when “white rice was a luxury item” according to their website. The simple menu consists of about 18 savory fillings such as ikura, tsukemono, and grilled salmon served with miso soup. The shop has two tables and counter seats with a great view of the ingredients, which are displayed like seafood at a sushi counter. Third-generation Yosuke Miura personally serves each onigiri as it is made, presenting it on a gorgeous woven bamboo tray, while traditional koto music plays in the background. The restaurant is the perfect stop near Sensoji temple in the historic Asakusa district and the colorful Kappabashi kitchenware district.

Nowhere serves unagi (freshwater eel) like Obana. The recipe for its kabayaki — fillets of eel that are steamed, charcoal grilled, and basted with a thick, rich, sweet-savory glaze — dates back to the times of the shoguns. Expect hour-long lines (especially on weekends) for the pleasure of sitting on a hard floor (thin cushions provided) at low communal tables, with a further wait while they dispatch the eel and slowly cook it to order. The anticipation is worth it, though. Obana’s unagi is widely agreed to be the best in the city.