Yes, there can be mild side effects if apple cider vinegar is used the wrong way. The benefits of drinking apple cider vinegar in the morning include better digestion and feeling fresh, while the benefits of apple cider vinegar on an empty stomach support metabolism when taken in small amounts. Drinking it without water or in excess may cause stomach irritation or throat burning. Conclusion: To enjoy the benefits of drinking apple cider vinegar in the morning, always dilute it with water and use it in moderation.