The quote says "Don't do school, eat your drugs, stay in vegetables". I realize the last part does not mean something like "remain in the box with potatoes" literally, so what does it mean?
A bit of context to where this comes from might help. This is pretty clearly a humorous transposition of phrases. It's mixing up "Don't do drugs, eat your vegetables, stay in school"
I don't think it's meant to have a specific meaning since it's likely just someone joking around.
This is kind of a malaphor, although not strictly one. This is one common saying that has had some of its words swapped around for effect. The full saying as it usually goes is:
Stay in school, don't do drugs, eat your vegetables.
Sometimes the order of the clauses is changed for emphasis.
That's the joke.¹
This is a deliberate corruption of the juxtaposition of three sentences: “stay in school”, “don't do drugs”, “eat your vegetables”. Each of these sentences is a thing that a parent might tell their child, or more generally advice that adults are expected to give to young children (the one about vegetables) or teenagers (the ones about school and drugs).
“Don't do school, eat your drugs, stay in vegetables” takes those three sentences and shuffles the complements around. “Don't do school” is not a common use of the verb do, but it is a straightforward use of the same meaning of do as the expression “[don't] do drugs”, where “do” means “participate in some action that involves the complement”. So it's just the opposite of the usual parental advice “stay in school”. “Eat your drugs” is also the opposite of the corresponding parental advice (“don't do drugs”), but it's weirder than the first part of the sentence because one does not normally “eat” drugs. Still, eat is a technically correct verb for drugs that are ingested through the mouth, such as weed cookies. Finally, “stay in vegetables” is so weird that it's completely meaningless. The humor comes in part from the escalation: the first part is wrong, the second is weird, and the third is not even wrong².
¹ A somewhat idiomatic expression which has the subtext “you didn't get the joke”.
² An idiomatic expression that basically means “meaningless”.
There are already answers explaining how this is a jumbling of a stock advice. I am not expanding on that. "Stay in vegetables" can have a perfectly valid meaning, however, outside of the obvious literal one (like staying in the vegetables aisle when a shooter is roaming the supermarket, or when you are asking where to do inventory next): namely short for "stay invested in vegetables". This can be advice to a grocer about what to keep in his offerings. It can be advice for somebody's investment portfolio. If you are into alliteration: what to keep in stock or what to keep in stocks.
The sentence wouldn't have taken the wind if it was just a random words swapping. The resulting phrase makes (an ironical) sense of its own.
There a common metaphor of living as a vegetable with the meaning of being deliberately passive, not pursuing any goals in life. Sitting in one place doing nothing, living a life not more productive than that of a plant. Such an attitude is commonly despised, so it makes the perfect sense in the resulting sentence: Don't go to school, do drugs, enjoy your life as a vegetable.