I get flour from a local windmill (super charming), lots of Asian and Indian ingredients from Amazing Oriental, beans and grains from the Turkish market, produce from an open-air market, and everything else from the "regular" grocery store. While it seems like a big pain in the asparagus, it was actually pretty cool to spend some time walking around in shops and checking things out. You don't need to speak the language to do this and you get familiar with how things are laid out, can take time to read labels and understand stuff, etc.
This. Supermarkets really just cater to mainstream food preferences. But, I've learned to love my weekly shopping rounds, and would not have it any other way.
Turkish/Moroccan stores do have cheap (often slightly misshaped but very tasteful) produce as well. And, do visit the Iranian delicatessen on the Kanaalstraat (= the street where pretty much all these ethnic foodstores are). This store is slightly pricier than the Turkish/Moroccan stores, but they have a the best mushroom selection in town, as well as a nut-and-seeds bulk bar.
Also, I have a weekly subscription to an organic produce bag. Every Tuesday, I pick up a bag with almost a weeks worth of greens and fruits for 7,50 euro. This bag is a one person bag, just for me, but there's different sizes and types available as well. I love the bags, for they are seasonal produce and give organic farmers a steady support/income, and I don't think they're expensive at all for what's in them. Most health food stores are pick up points for these, and you can fix your subscription there as well. :)