It most likely did and you did not notice. When you finish the first level, you get +10 explo as stats, not bonuses. Etc etc... it's not shown as a green bonus in the stats windows, it's just +10 added as your raw stats
Bonuses are applied at the moment you reach the level of credo for that bonus (i.e. if Forager is your first credo, after finishing 2 quests you get the +10 exploration etc. And lose that bonus if you abandon a quest and drop a level). When you finish the credo, you unlock the very last bonus (all previous are already applied) and unlock possibility to pursue next credo.