I must start by saying that the average quality of food in Japan is the best I know; this includes Japanese and foreign food. However, there's two things that Japan can and should improve: coffee and cheese.
The usual degree of coffee beans' roasting in Japan is quite dark (and often uneven) for my taste. However, some coffee roasters do a good job.
Obscura Coffee Roasters: Good
I visited the location near Akihabara. Unfortunately it is now closed. They also have a fantastic pour over (I think they use Hario V60). There are two other locations in Tokyo according to google maps, which I never went to, but I am sure they are also good.
1 Chome-9-16 Sangenjaya, Setagaya-ku, Tōkyō-to 154-0024, Japan
4 Chome-4-28-9 Taishidō, 世田谷区 Setagaya-ku, Tōkyō-to 154-0004, Japan
ROAR COFFEEHOUSE & ROASTERY: Good (last visit October 2019)
Very nice shot. They have two options: single origin and a blend. I obviously had the single origin. The presentation was also quite unique, they use mini-sparkly-wine glasses. Probably the best espresso in Chuo City area.
2 Chome-19-11 Hatchobori, Chuo City, Tokyo 104-0032
Coffee Valley: Good (last visit May 2019)
They try hard to make their coffee excellent. Although I usually comply of Japanese coffee to be too dark/bitter, this coffee shop goes in the opposite direction: a little too sweet and pungent. However, it's still good.
2-chōme-26-3 Minamiikebukuro, Toshima-ku, Tōkyō-to 171-0022
All Seasons Coffee: Good (last visit October 2019)
The espresso was good. At the beginning, I was skeptical because the shop looks like the standard Japanese "wanna-be" coffee shop. However they have a nice espresso shot. There's no option to choose different beans, but they use single origin.
Although speed doesn't influence my rating, I must say that the service is quite slow, so avoid it if you are on a rush.
1 Chome-6-1 Nishiwaseda, Shinjuku City, Tokyo 169-0051
Blue Bottle Coffee at Ikebukuro: Good (last visit May 2019)
Blue Bottle Coffee at Shinjuku: Descent (last visit October 2019)
Blue Bottle Coffee at Roppongi: Drinkable
They are not very consistent. People at Ikebukuro do make a better job. It might be because they are located just a few steps away from Coffee Valley? Update: I downgraded their rating at Shinjuku to descent; their quality has definitely decreased in the last couple of years. On the other hand, the espresso at the Roppongi location was drinkable at best. There are other locations, I haven't visited them.
2-chōme-23-7 Minamiikebukuro, Toshima-ku, Tōkyō-to 171-0022
4丁目-1-6 Shinjuku, Shinjuku-ku, Tōkyō-to 160-0022, Japan
7-chōme-7-7 Roppongi, Minato-ku, Tōkyō-to 106-0032
Ammonite Coffee Market: Descent (last visit May 2019)
The taste was good, but a little watery. My guess is that they grind the beans rather coarsely. It's the best option in the Todai area.
〒113-0033 Tōkyō-to, Bunkyō-ku, Hongō, 7-chōme−2−6 シンセイビル1F
Verve Coffee: Descent (last visit November 2019)
I went there a few years ago (maybe in 2017) and it was bad, however a friend suggested me to visit it again. I did so, and it has significantly improved. Although the espresso was slightly bitter, I marginally prefer Verve rather than Blue Bottle at Shinjuku station, and both are literally 1 minute away from each other.
NEWoMan Shinjuku 2F 5-24-55, Sendagaya, Shibuya City, Tokyo 151-0051
Funglen Tokyo: Descent
I went there only once. I can't say much about it.
1丁目-16-11 Tomigaya, Shibuya-ku, Tōkyō-to 151-0063, Japan
Sarutahiko Coffee Omotesando: Drinkable/Trap
The reason why I decided to visit this place was that I found not only very good reviews, but also nice looking pictures of their latte art, which is in general a good indicator of good espresso (plus good milk and careful baristas). However, the espresso was barely drinkable. I did not find a better espresso in that area.
〒150-0001, 4 Chome-3-3 Jingūmae, Shibuya-ku, Tōkyō-to 150-0001, Japan
Streamer Coffee Company Kayabacho: Trap (last visit October 2019)
It's my fault for keep trying cafe chains. They don't have espresso; instead, they serve something called "triple ristretto," so I obviously ordered a double of that thing. And as expected, it was very bad: dark, bitter, and the crema was too foamy. This makes me believe that they use pressurized baskets.
〒103-0016 Tokyo, Chuo City, Nihonbashikoamicho, 11−8 1F
Cawaii Bread & Coffee: Trap (last visit October 2019)
I didn't even try it. Why? The beans looked clearly cheap: super oily and large. Most likely robusta. Also, their espresso machine is home-grade.
〒104-0032 Tokyo, Chuo City, Hatchobori, 2 Chome−30−16 T&Yビル 1F
Kurasu Kyoto: Good
It is near Kyoto station. I had a hard time classifying this coffee shop between good and descent.
552 Higashiaburanokōjichō, Shimogyō-ku, Kyōto-shi, Kyōto-fu 600-8235, Japan
Sentido: Descent
The first time I went there, the espresso was good, However, it was barely descent on the second time I visited. I also had a (if I recall correctly) french press from them, and I didn't enjoy it.
Japan, 〒604-8187 Kyōto-fu, Kyōto-shi, Nakagyō-ku, Sasayachō (Higashinotōindōri), 京都府京都市中京区笹屋町445
Slow Jet Coffee: Drinkable
I will include it on my reviews because of its location: Chion. Since there are not other options in that area, all tourists will eventually end up right at their door.
Japan, 〒605-0825 Kyōto-fu, Kyōto-shi, Higashiyama-ku, Shimokawarachō, 東山区高台寺下河原町526 高台寺境内
Lilo Coffee Roasters: Great (last visit December 2019)
Based on my experience, the best coffee shop in Japan and probably Asia. You can select from a list of more than 15 different single origin beans and choose a lighter or darker roasting. Unfortunately, they don't have other locations anywhere else.
Japan, 〒542-0086 Ōsaka-fu, Ōsaka-shi, Chūō-ku, Nishishinsaibashi, 1 Chome−1−10-28 心斎橋Mビル
Morning Glass Coffee: Good
The espresso was very good, one can easily see they know what they are doing. Unfortunately there is only one option of beans for espresso, while they have several options for pour-over. Nevertheless, I enjoyed the coffee and if they had more than one option of bean for espresso, I would rate them as great. Their food is good for brunch, and they have my favorite 'mainstream' Japanese beer on tap: Heartland.
3 Chome-2-14 Azuchimachi, Chūō-ku, Ōsaka-shi, Ōsaka-fu 541-0052, Japan
R39bar Espresso Mania: Drinkable
Despite its name, don't expect much. Moreover, it's located just 3 blocks north of Morning Glass Coffee, which is a much superior option. So I would definitely avoid visiting again.
2 Chome-5-11 Awajimachi, Chūō-ku, Ōsaka-shi, Ōsaka-fu 541-0047, Japan
The Otherside Coffee: Drinkable (last visit December 2019)
The place looks nice, but the espresso isn't. However it's probably the best option nearby Shin-Osaka station.
〒532-0011 Osaka, Yodogawa Ward, Nishinakajima, 2 Chome−15−12 カジサンビル2F
BROOKLYN ROASTING COMPANY Kitahama: Trap
This place has a large number of reviews and they are usually good reviews. However I can't even say it's drinkable. The espresso was short and under-extracted, yet bitter. The barista didn't know what he was doing. I checked on their website, and it looks like they are affiliated with an American roasting company with the same name. There is another location in Namba. I didn't visited it.
2 Chome-1-16 Kitahama, Chūō-ku, Ōsaka-shi, Ōsaka-fu 541-0041, Japan
I haven't been able to find good espresso in Kobe. I will include two places that I consider drinkable.
ZEF Coffee Motomachi: Drinkable/Trap
I found good reviews for this place, but when I visited the shop the espresso did not match my expectations.
3 Chome-1-2 Sannomiyachō, Chūō-ku, Kōbe-shi, Hyōgo-ken 650-0021, Japan
Honolulu Coffee: Drinkable
Right next to Kobe-Sannomiya station.
Japan, 〒650-0012 Hyōgo-ken, Kōbe-shi, Chūō-ku, Kitanagasadōri, 1 Chome−8−3 エンジェル松浦
Obscura Coffee Roasters: Good (last visit December 2019)
This Tokyo-based coffee roaster has now two branches in Hiroshima city. By far, this is the best option in the whole city.
1-10 Otemachi, Naka Ward, Hiroshima, Hiroshima Prefecture 730-0051, Japan
3-1 Hondōri, Naka Ward, Hiroshima, 730-0035
Progress Life Style Ceffee: Good (last visit April 2021)
They have a nice espresso shot, although only one option for beans. It's closer to Hiroshima Station compared to any of the Obscura branches.
1-15 Shintenchi, Naka Ward, Hiroshima, 730-0034
Park South Sandwich: Trap
Although the cafe looks very nice and professional, the espresso was horribly bitter. If you are looking for an espresso, Obscura Coffee is much better and is located just a few minutes walk away.
The sandwiches seem ok (i.e. standard for Japan), although I didn't taste them. The pour-over was ok, they have 3 levels of extraction (I don't actually know what they mean by that), and I got the lightest one. It refreshed my mouth from the bitterness of the espresso.
1-26 Nakamachi, Naka Ward, Hiroshima, 730-0037, Japan
The Coffee Bar: Good (last visit December 2019)
Unexpectedly, the coffee shop right outside tiny Okayama station has good espresso! It's just 3 minutes walk from the station. It's ideal if you have a train transfer.
15-1 Ekimotomachi, Kita Ward, Okayama, 700-0024