The mutuals have created websites to help guide borrowers through the process with various options being available.
Both lenders emphasised that it was better for borrowers to repay as much as they could afford, and their customers will be directed to calculators to make clear the financial impact of the change as payment breaks will continue to accrue interest.
The moves come as the Financial Conduct Authority (FCA) confirmed earlier this month how the three-month extension to mortgage payment holidays would work for those re-applying and those making their first claim.
While payment holidays will not be reported on credit files, lenders can use them to assess mortgage affordability and many are doing so already.
Nationwide said it was offering new three-month mortgage payment breaks as well as providing the option to make partial payments towards a mortgage.
Its members already receiving payment support will be contacted prior to it ending and directed online.
Additional measures coming before the end of June include extending mortgage payment breaks to buy-to-let landlords.
Nationwide said it is encouraging landlords to apply for the breaks if their tenants are struggling to pay rent due to Covid-19, and where possible to pass on the benefit.
It also reiterated that no mortgage member falling into arrears as a result of Covid-19 will lose their home until the end of May 2021 if they work with the society to get their finances back on track.
Nationwide director of mortgages Henry Jordan said: “Many people are still experiencing financial difficulties as a result of the outbreak and we want to support where we can.
“While we would always encourage people to pay what they can, there are cases where this is just not possible.
“The unknown timeframe of how long this impact will last has led us to halting repossessions linked to Covid-19 until the end of May 2021 to give our members as much reassurance as we can.
“All that we ask is that our members continue to engage with us so that we can agree with them the best way to help them.”
Leeds Building Society has introduced the ability to repay some or all of borrowers’ deferred repayments by lump sum immediately for those who are able to.
The mutual will also be recalculating the monthly repayment, to ensure deferred repayments are spread over the remaining term of the mortgage or giving the option to extend the mortgage term.
It is also waiving any arrears fees until the end of June and will not seek possession of any properties before the end of October, unless the borrower requests it.
Borrowers will be contacted by letter or email at the end of their mortgage payment holiday, which will explain the impact on their repayments and any action they need to take.
It will direct them to the relevant part of the website which will have the latest information and guidance and will direct them to their options.
“While it remains best advice to pay your mortgage if you can, we know some families who’ve taken a payment holiday already will welcome being able to now defer repayments for up to six months,” said Leeds Building Society chief customer officer Jaedon Green.
He continued: “The pandemic is a worrying time for so many people, about their finances and much more.
“We’ve tried to make the process as straightforward as possible for anyone who’s taken a mortgage payment holiday since March or is thinking they may need to in the coming months.
“While we’ll continue to work with any borrowers experiencing longer-term financial difficulties, customers who applied for a mortgage payment holiday as a precaution should be aware the deferral of monthly payments or extending the mortgage term results in additional interest payable over the life of the mortgage.”