A major challenge in bisulfite sequencing is the degradation of DNA that takes place concurrently with the conversion. The conditions necessary for complete conversion, such as long incubation times, elevated temperature, and high bisulfite concentration, can lead to the degradation of about 90% of the incubated DNA.  Given that the starting amount of DNA is often limited, such extensive degradation can be problematic. The degradation occurs as depurinations resulting in random strand breaks. Therefore, the longer the desired PCR amplicon, the more limited the number of intact template molecules will likely be. This could lead to the failure of the PCR amplification, or the loss of quantitatively accurate information on methylation levels resulting from the limited sampling of template molecules. Thus, it is important to assess the amount of DNA degradation resulting from the reaction conditions employed, and consider how this will affect the desired amplicon. Techniques can also be used to minimize DNA degradation, such as cycling the incubation temperature.
In 2020, New England Biolabs developed NEBNext Enzymatic Methyl-seq  an alternative enzymatic approach to minimize DNA damage.