Since 5AD, Arabic script was used to write Malayalam. This was called "Arabimalayalam" and is still used in Kerala. The 28 Arabic letters couldn't render 53 phonemes of Malayalam, so new letters were created for it !
"Muhyadheen Mala" is the first book written in Arabimalayalam
In the internet age, Latin script is used to write Malayalam (aka Manglish). English can't render all the phonemes of Malayalam, so letters are pronounced differently according to context. "enna" can be both എന്നാ and എണ്ണ.
There are christian prayer books written in Manglish !
Similar to Arabimalayalam, there is also "Suriyani Malayalam" which uses Syriac script to write Malayalam. It originated among Saint Thomas Christians of Kerala, but is not widely used nowadays. Like Arabimalayalam, new letters to accomodate Malayalam phonemes were created.