How do airports differentiate supplements from drugs?

I brought some creatine and BCAA powder, along with multivitamin pills on a few flights ( from Italy to Spain and back, from Czech Republic to Italy and back) in some containers, so not in the original packaging. I had it in my hand luggage (backpack) and when they saw it on the x-ray they did a drug test by swiping some kind of paper/plastic stripe on my hands, on the bag and clothes. It of course had negative result, so they were ok and didn't ask anything and I just went on.

I assume you will have a similar experience, you will get tested for drugs but don't worry no crazy situations will happen (this of course if you don't have any traces, so be sure to don't go around with drug users with your bag) and you won't even loose much time. This at least in Europe, not sure about other places with higher drug problems. (in many countries small amounts for personal use are allowed, but I don't think you can bring them on the plane)

It might be no problem, but it might also attract unwanted attention and unwanted delay. Why not keep it in the original packaging and mix it to your recipe at your destination?

I once took six 15 oz. packages of the meal supplement Soylent in my carry-on for a domestic US flight. The TSA officers tested the outside of each package with some sort of chemical swabbing test. Two of the packages actually came up positive. They did mention the test tends towards false positives. They discarded those two packages and let me continue. All in all the extra testing took almost half an hour. So I would recommend putting any supplements in your checked luggage if possible to avoid the hassle.

If you're going to a big enough airport in a developed country they generally have an array of methods to test these substances. Chemical or electronic swab test, sniffer dogs. When they find you suspicious they can test your protein on the spot for drugs.

You do need to be careful when traveling to small local airports. They might not have the proper equipment to test your protein and can hold you there for some time while they get in contact with a lab.

If they do find you suspicious the best thing you can do is fully cooperate. Tell them what it is and why is it packaged in this way. Offer them to smell it if they want to. (My protein powder smells like chocolate milk, I have no idea about yours.) If it's not a drug you won't be in any trouble.

While others correctly have answered how any suspicion of carrying traditional illegal drugs will be handled. It should not be a worry to you.

There is something else that you need to take into consideration when carrying supplements across borders and that is the fact that even brand supplements aren't always clean, they can contain substances considered doping.

Carrying doping substances across borders can, depending on juridiction, be a crime, often considered a far bigger crime than being in possesion of the similar amount on the street.

While it is unlikely that traces turn up in a scan, but theoretical it could, and if it does, it could get you denied entrance or similar.

If you buy the same supplement in a shop in the country you visit you will not run the same risk.

I've carried various white powders through security and customs, the only thing that has ever been looked at was a bottle of light salt (half sodium chloride, half potassium chloride) and that was in it's original packaging--and that was TSA, not customs. I have always had at least one original container (which is obviously medical in nature) although I have also carried stuff for which I do not have the original containers (a mixture of many things, to bring all the original packaging would be a suitcase).

I've also gotten various degrees of swabbing when I brought liquids through security, although I've always packed the original containers also--generally one look at the original package and they're obviously just going through the motions.