The results track with sales results at many of the major fast-food chains, which are struggling to find the right recipe to woo younger U.S. diners who increasingly are seeking fresher, healthier food.
"More and more, food quality - not just low price - is emerging as a deciding-factor for many Americans," said Tod Marks, senior projects editor for Consumer Reports.
Marks called results Consumer Reports' poll of 32,405 subscribers, a "wake-up call" for the industry: "Our survey clearly shows the big guys need to respond."
The top-rated hamburger restaurants were In-N-Out Burger, The Habit Burger Grill and Culver's. McDonald's Corp, the world's largest chain but a laggard when it comes to taste, finished behind 20 others, including Jack in the Box Inc, Wendy's Co and Burger King Worldwide Inc.
Yum Brands Inc's Taco Bell, which spiced up U.S. sales with Doritos Locos Tacos and breakfast, finished at No. 8 among Mexican chains behind Rubio's Fresh Mexican Grill, Chipotle Mexican Grill and Qdoba Mexican Grill.
Yum's KFC also landed the eighth position in the chicken restaurant category behind Chick-fil-A, Boston Market and El Pollo Loco.
The nation's top pizza chain was Papa Murphy's Take 'N' Bake Pizza, ahead of bigger rivals Papa John's International Inc and Domino's Pizza Inc.
Portillo's Hot Dogs, Jason's Deli and Firehouse Subs were leaders in the fragmented sandwich category. Pei Wei Asian Diner was No. 1 in the emerging Asian segment.
Chick-fil-A, which has stirred fiery debate with its anti-gay marriage stance, also led in service and clean surroundings.
Del Taco got first place for "more for your money".
Privately held Subway, whose pitch man Jared Fogle lost more than 200 lbs on a diet of the privately held sandwich seller's food, was No. 1 for healthful choices, followed by Jason's Deli and Panera Bread Co.
When it comes to unhealthy "foods to fear," Consumer Reports called out Firehouse Subs' large Sweet Thai Chili Pork Sub that clocked in at 1,541 calories, 95 grams of fat and 3,458 milligrams of sodium.
U.S. dietary guidelines recommend individuals consume no more than 2,000 calories, 65 grams of fat and 2,300 milligrams of sodium daily.