Azo dyes are challenging to degrade due to their chemical stability, structural diversity, and the toxicity of their degradation products, which can be more harmful than the original compounds. Their strong binding to fibers and xenobiotic nature further complicate biodegradation efforts.

The azo bond (-N=N-) is highly stable and does not easily break down through natural processes. Additionally, most azo dyes have complex aromatic structures that resist microbial and chemical attacks. These dyes are synthetically designed to be durable and resistant to light and chemicals, which makes them harder to break down. This, combined with the potential formation of toxic by-products during degradation, makes them particularly challenging to degrade.

The (-N-N-) bonds either triple or double bonds make dyes stable and their degradation products are also carcinogenic and mutagenic creating more challenges in degradation.