"If he does not eat his tomato, he does not get sugar."
Translation:Wanneer hij zijn tomaat niet eet, krijgt hij geen suiker.
You probably got the verbs mixed up. This is only something I have observed so I may be wrong. Hopefully someone with more knowledge will come by later.
I have noticed in if-then conditionals, the verb from the condition (the "if" part) is at the end of that clause and the verb from the consequence (the "then" part) goes at the beginning of the clause.
This is correct! The verb always goes last in a subordinate clause, but whether the verb goes first or second in an independent clause depends on which clause goes first. If the subordinate clause is first, the verb will go at the front. If the independent clause is first, however, the verb will go in its normal second position. :)
That answer is incorrect because of your placement of "niet." In Dutch, whenever "niet" negates a noun that is a direct object, it must go after that direct object (just like in German). As a result, it would be "Als hij zijn tomaat niet eet, krijgt hij geen suiker." Otherwise the answer is correct. :)