Here, nutrition experts share the best time to take probiotics, plus the best foods to take them with, how to add probiotic-rich foods to your diet, and more. “Some studies suggest that the best time to consume probiotics is with or after meals,” said Mia Syn, M.S., R.D.N., owner of Nutrition by Mia . Given that they’re digestion-centric, to consider meal time when taking probiotics is natural. On the other hand, taking probiotics with food may also help them survive their digestive travels. Keiser said it’s best not to take probiotics if you’re also on antibiotics, which can kill off probiotics and reduce their efficacy.