The present study was initiated to investigate the influence of oral application of charcoal, sauerkraut juice and humic acids on specific gastrointestinal microbiota and selected enzymes, electrolytes, and substrates in the blood of dairy cows fed GMO feeds containing glyphosate. A total of 380 Schleswig Holstein cows suffering from symptoms of chronic botulism were fed sequentially with 400 g/animal charcoal daily for 4 weeks (weeks 1-4 of the study), 200 g/ animal charcoal (weeks 5-10 of the study), 200 g charcoal and 500 ml Sauerkraut juice/animal (weeks 11-14 of the study), 120 g/animal humic acids (weeks 15-18 of the study) 200 g charcoal and 100 mL Aquahumin/animal (weeks 19- 20 the of study), or 100 g charcoal and 50 mL Aquahumin (weeks 21-22 of the study) followed by 4 weeks without any supplementation. There was a significant reduction of glyphosate in urine following supplementation with a combination of 200g charcoal plus either 500 mL sauerkraut juice or humic acid. From all of the parameters investigated in blood and urine, distinctive effects were only seen as a lack of manganese and cobalt and a significant reduction of creatinine excretion by urine. All other measured parameters such as creatine kinase (CK), alkaline phosphatase (AP), glutamate dehydrogenase (GLDH), glutamate oxaloacetate transaminase (GOT), and cholesterol, urea, and blood creatinine) were not significantly changed. A significant increase of fecal Gram-negative bacteria and enterococci were only seen at week 8 (200 g charcoal/d) and week 20 (200 g charcoal+100 mL Aquahumin). In conclusion, a charcoal-sauerkraut juice combination and humic acids reduced glyphosate excretion by urine and led to the improved health of animals.