Making the world better, one answer at a time. The main difference between filtrate and urine is the chemical composition of the two. Filtrate has almost all the substance that blood plasma has except blood proteins while urine only contains waste substances.aking the world better, one answer at a time. The main difference between filtrate and urine is the chemical composition of the two. Filtrate has almost all the substance that blood plasma has except blood proteins while urine only contains waste substances.