The 11 Best Bagels in San Diego, Ranked

Desperado Bagels started small, the way a lot of good San Diego food does. Gerry Giuliano ran it as a Sunday-morning pop-up out of his Ocean Beach bungalow, and it kept growing until it moved into the bakery on Hancock Street in the Midway District. Sunday morning is still baking day, and this is the bagel every other shop on this list gets measured against.

Here's what the fuss is about. These are big, generously sized bagels with no traditional hole to speak of, a firm crust, a chew with real definition and a deep, malty flavor. In San Diego Magazine's 2025 blind tasting, Desperado scored 9.4 out of 10, the top mark of the field, and took both Best Overall and Best Flavor. The judges called it "damn good bread from skilled, no-frills baking," noted a potent yeasty aroma, and said it stands on its own without needing a spread.

Take them up on that. Start with an everything bagel, plain. Fans of the place talk about the size, the defined chew and the crisp crust, and above all about the everything seasoning, which goes on with unusual force. Cream cheese can wait for bagel number two. A bagel like this has earned a minute on its own.

Now the planning. The Hancock Street bakery bakes on Sunday mornings and sells out, so get there early and check hours before you go. The rest of the week, Desperado bagels land at the PorchLight Coffee counter at 4865 Cass Street in Pacific Beach, which is a separate spot from the bakery. Stock at PorchLight changes from day to day, so think of the Don Poblano sandwich or a flavored schmear from the case as a bonus when you spot one. The everything bagel is the anchor either way.

So yes, it takes a little more planning than the shop down the street. That's the price of the best bagel in town, and it's worth setting a Sunday alarm for.

Every single bagel at New Wave Bagel is sourdough. This Encinitas shop on Coast Highway naturally ferments all of its dough, then hand-rolls, boils and bakes the bagels fresh daily, using organic, non-bromated flours from Central Milling and King Arthur.

The people behind it come from bread. Co-founders Cheryl Storms, who runs the front of house, and Matt Cardwell, the culinary director, are both Wayfarer Bread alumni, and they built a following with pop-ups in Encinitas and Bankers Hill before opening the permanent shop on the coast.

That bread background shows up in the bagel. In San Diego Magazine's 2025 blind tasting, New Wave scored 9.2 out of 10 and won Best Sourdough Bagel. Judges praised big, stretchy air pockets inside a deeply caramelized, crunchy crust with a pretzel-like quality, and a few of them noted the texture wanders from a traditional bagel. That's the adventure here. If Desperado is the purist's pick, New Wave is the bread lover's.

Save room for the schmears. The cream cheese program made Schmear Finalist at BagelFest 2026, and the lineup has included chili crisp scallion, honey walnut and a smoked-fish schmear made with locally caught fish the shop cures in-house. The praise keeps returning to that airy chew, the caramelized crust and bold seasonal flavors, and to a bagel that holds its own under all those creative toppings.

The menu changes every month, so the flavor you fell for in spring may have moved on by summer. The tasting judges singled out the marble rye as a standout, so grab it if it's on the board. Prices sit on the higher side for a daily habit, so think of it as a weekend treat and a great excuse for a drive up the 5.

Yes, one of the best bagels in San Diego comes from a shop with "Donuts" in its name. Nomad Donuts started as a small doughnut shop on 30th Street and grew into its current home on University Avenue in North Park, and these days its Montreal-style bagels are a big part of the draw.

Montreal-style is its own thing. Nomad boils its bagels in agave-sweetened water, which gives you a softer, denser bagel than the New York kind, a little sweeter, with a yeasty aroma. In San Diego Magazine's 2025 blind tasting, Nomad scored 9.1 out of 10 and took Best Sweet Bagel. One judge compared the texture to a "memory-foam mattress (but in the best way)," and most of the panel "devoured" them, even though the style departs from tradition.

The rosemary sea salt bagel is the one everybody brings up, and plain cream cheese is all it needs. Beyond that, fans point to a crisp exterior around a dense chew, creative sandwiches, and a vegan lineup with real range, so a plant-based friend gets actual choices.

If you grew up on New York bagels, go in knowing Montreal-style runs sweeter and denser by design. That's the pleasure of it, and it's how a doughnut shop ended up at No. 3.

A little planning helps. Nomad is closed Mondays and Tuesdays, parking along University Avenue takes some patience, and the line builds during busy stretches, so an early start is your friend.

Mission Bagel is a brother-and-sister operation on Garnet Avenue in Pacific Beach, and it turns out one of the most dependable New York-style bagels in the city. Gabe Rubin founded it and bakes with his sister Hannah, after leaving another job to go all in on bagel-making.

One thing to know right away: Mission is closed on Saturdays for Shabbat. It's a useful planning note, and it also tells you something about the people running the place.

The bagels have won over the pros. In San Diego Magazine's 2025 blind tasting, Mission scored 8.2 out of 10, and judges described a satisfyingly chewy interior, a well-developed crust and a restrained flavor with a gentle tang. They also called out a bouncy, stress-ball texture with a nostalgic soft-pretzel quality. Recent reviews line up with that, and add fresh bagels, bialys, friendly service and breakfast sandwiches to the case for going.

Start with a poppy or everything bagel and plain cream cheese. Then take a real look at the bialys before you fall back on your usual order. They're easy to overlook, and Mission's come up often in reviews. When you need more than cream cheese, the breakfast sandwiches have a following of their own.

Plan for a small, busy shop. Flavors sell out, seating is limited, and at the morning rush a single order can take about 15 minutes, so come early or come patient. Garnet Avenue parking is tight. Mission also runs a food truck at the corner of Ingraham and Grand, a second way to get your fix in PB.

Seventy-two hours. That's how long Inglourious Bagels & Coffee in Carlsbad slow-ferments its dough before the bagels are baked, fresh every day. The shop also skips seed oils and uses a custom water profile, and that kind of care is the reason it earns a spot this high.

The praise tends to circle back to the chew and the seasoning, and a couple of the best compliments come with a New York accent. One reviewer called these the closest bagels to New York they'd found in San Diego, and a self-described native New Yorker said the same thing. In a city full of transplants with strong bagel opinions, that's a serious endorsement.

Start with an everything or sesame bagel, plain, then come back for the bacon, egg and cheese, the sandwich people mention most. The menu has a couple of personality picks too, the Latke Loco and the Meksikaner, for when you want to wander past the classics. Inglourious was also among the San Diego shops recognized at BagelFest 2026.

Here's the practical case for it: of the top five, it's the one bakery that's open every day of the week, so it's the easy answer on a Monday or Tuesday when New Wave and Nomad are closed. There's outdoor seating, and the early-morning service gets good marks. Loaded sandwich orders add up quickly and the counter can back up at times, so settle on your order before you reach the front.

101 Bagels & Subs is the Oceanside counter that handles breakfast and lunch in one stop. The menu at this North Coast Highway shop is organized into sections with names like "Fresh Baked Authentic Bagels," "Old Tyme Favorites" and "Bagel Melts," with fruit smoothies on the side and a full run of subs and deli sandwiches for later in the day.

The love here is for the basics, done generously. Regulars talk about fresh bagels, big breakfast sandwiches and friendly service, and it has the steady repeat crowd of a true neighborhood spot. It's also one of the better values on this list.

One tip will make your order better: tell them how you want it toasted. The shop doesn't assume, so if you like your bagel dark, say "dark." From there, a classic bagel with cream cheese is the easy call, and the bacon, egg and cheese is the one for a hungry morning.

Where the shops above it lean into long fermentation and signature styles, 101 is all about a reliable, hearty breakfast. Lines build during the morning rush, and weekend and holiday hours are worth a quick phone call to confirm.

Mike Rabinowitz grew up around the corner bagel shops of the New York area, and when he opened Marigold Bagels in North Park in 2022, he set out to recreate them. He's Brooklyn-born and trained in organic chemistry, and he developed his own bagel recipe to get there.

The process is about as careful as you'd hope from a chemist. It starts with high-gluten flour and ultrapure water, then comes hand-rolling, a long cold fermentation, a boil in malted water and a bake in a deck oven. All of it happens in-house at the El Cajon Boulevard shop, with no central commissary, and the whole thing takes days.

The case goes well past bagels: bialys, chocolate babka, pumpernickel, house cream cheese schmears, a vegan cashew spread and Lower East Side-style half-sour pickles. Fans single out the crust, the classic flavors, the bialys and a proper chewy bagel texture. The shop also carries San Diego Magazine Best Restos badges from both 2025 and 2026.

Go for sesame, poppy or salt while they're warm, and save the weekend for a bialy or some chocolate babka. On method and range, Marigold stands with anyone on this list. The lines and the small room are the things to plan around: seating is limited and weekend specialties sell out, so an early arrival gives you the best shot at the full case.

PopUp Bagels on Pearl Street in La Jolla serves its bagels hot and whole, in batches, and you tear them apart and drag them through the schmears. The company trademarked the format as "Grip, Rip and Dip," and says the idea came from watching customers buy bagels by the dozen and set their schmear cups straight into the car's cup holders.

The salt bagel and the schmears get the most love, and the scallion schmear comes up again and again. There's a rotating weekly schmear too, with flavors like strawberry shortcake and pesto butter, and PopUp runs national collaborations, including Drew's Berry-More Butter with Drew Barrymore and a Mirrorball Medley tie-in with Dancing with the Stars.

Consistency is where PopUp shines. On our scoring, no shop on this list was steadier, and only one topped it on execution. It sits at No. 8 mostly because the format is narrow by design: the menu is short and there are no sandwiches at all. If you want a bagel sandwich, look higher up the list. If you want a warm bagel to share with friends or bring to the office, this is your stop.

The shop closes at 4 p.m., so plan it as a morning or early-afternoon run. Bundles add up quickly, so decide how many people you're feeding before you order.

Carrot lox on a bagel is the order at Ben & Esther's Vegan Delicatessen, a fully vegan deli on El Cajon Boulevard in the College Area. It's the San Diego location of a Portland, Oregon deli of the same name, and both shops are vegan from the bagels to the soup.

The menu reads like a full deli counter. Alongside the carrot lox, there's housemade matzo ball soup, tofu egg salad sold by the pound and a case of vegan schmears. It's the only full vegan bagel-and-deli program in the county, and the press has noticed, with features in Eater, VegNews, Vegetarian Times and Insider.

People who love it talk about the schmears, the carrot lox, the bagels themselves and the kind service. Ask the counter which schmear goes best with the lox and take the advice. It's the easy pick for a vegan friend, a dairy-free relative or anyone curious about what a plant-based deli can do.

It trails the top of this list on pure bagel craft, and it makes up for that with something no other shop in the county offers. Popular items sell out, so aim for earlier in the day, and grab some tofu egg salad to take home while you're there.

If you love a big menu, Memo's Bagel Cafe on Jamacha Road in El Cajon has plenty to choose from. The flavor board has run to zaatar, sriracha habanero, spinach parmesan and muenster bagels, and the cream cheeses go from garlic chive all the way to fig and goat.

Where Marigold goes deep on the classics, Memo's goes wide. The praise centers on fresh bagels, lots of flavors, quality ingredients and breakfast sandwiches with generous combinations, all served with the friendly warmth of a neighborhood spot that has plenty of regulars.

So use the range. A zaatar or sriracha habanero bagel with a cream cheese you've never tried is the fun order here, and the breakfast sandwiches are there when you need something bigger. Feeding a crowd or the office? The baker's dozen is a good value.

The morning rush can back up the counter and waits can run long, so pick a first choice and a backup before you reach the register. That little bit of prep makes the whole visit smoother, and it leaves more time to argue over the next flavor.

I Love Bagels — Oceanside is a neighborhood bagel shop in the Home Depot Square shopping center on Vista Way, and it keeps things classic. The bagels are boiled and baked in-house, and the homemade cream cheese spreads are what the shop points to as its signature.

Locals keep coming back for fresh boiled bagels, classic breakfast sandwiches and those house cream cheeses. It's a repeat-visit kind of place, the neighborhood shop you can build a weekday routine around without thinking twice.

An egg, rye or everything bagel with one of the house cream cheeses is the order. Breakfast sandwiches and deli sandwiches round out the counter when you want something heartier or need to pack a lunch.

Next to the more expressive shops higher on this list, this is a straight-ahead, conventional bagel, and a reliable one. Between this shop on Vista Way and 101 Bagels & Subs on North Coast Highway, Oceanside has two solid bagel counters on this list. Busy stretches can slow the line, so leave a little cushion in your morning. The shop closes for Thanksgiving, Christmas and New Year's Day.