I'll echo all the other great comments about selection and price. Even if the lines were short, it'd always be a struggle to get in and out of that place in less than an hour because the rows of produce are just so inviting. Hopefully things will become a bit more manageable once the new store in West Berkeley opens, but until that happens, I've learned to go outside of the peak times to avoid long lines.
These times, according to my experience, are:
Any weeknight, except Friday. Mondays are particularly bad, and the half hour before closing time (8 pm) can be atrocious. If you must go on a weeknight, I've had pretty good luck between the hours of 6 and 7 pm.
Around lunchtime.
Most of the weekends, except for some of the shoulder periods (near opening and closing).
I remember the Whole Foods in NY (when there was only one) used to have a sign advising people when the lines tended to be shorter. Perhaps BB should do the same.
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