How long do Side effects of azithromycin like nausea, diarhea and bad stomach upset last? 6 days since last dose and I still have side effects.

Bowel health. The medication should be out of the system by now, but the effect on healthy gut bacteria will persist for months. Taking a probiotic, which is available in many forms without a prescription, may help reduce symptoms. If not, or if symptoms are severe, then a stool test to rule out 'C diff' infection is important because it often follows antibiotic treatment, and can be fatal.
Variable. Symptoms vary from one person to the other. I will suggest you try some over the counter meds like Prilosec for symptom relief.