The Home Secretary confirmed a few months ago that people could apply after that deadline, but they must have “reasonable grounds to apply late”.
Existing limited or indefinite leave to enter or remain
Those with limited leave can apply to the Scheme any time after their limited leave expires so long as they have reasonable grounds for applying late in line with the overall guidance. Those with indefinite leave do not need to apply at all, but there may come the point in time that they want to do so to acquire the additional rights that come attached to settled status. They can apply late to the scheme so long as they demonstrate reasonable grounds for missing the deadline, in line with the guidance.

Pre-settled to settled status
Although the headline Settlement Scheme deadline is 30 June 2021, the Scheme was never going to close on that date fully. The Home Office intends for it to remain open for years to come for those with pre-settled status to apply to upgrade to settled status.
As things stand, the deadline for those with pre-settled status to apply for settled status will be unique to the individual: it is the expiry date of their pre-settled status. So late applicants can be those who fail to meet the deadline of 30 June 2021 to apply for initial status, but also those who miss their personal deadline to “upgrade” their status in the years to come.
Although the headline Settlement Scheme deadline is 30 June 2021, the Scheme was never going to close on that date fully. The Home Office intends for it to remain open for years to come for those with pre-settled status to apply to upgrade to settled status.
As things stand, the deadline for those with pre-settled status to apply for settled status will be unique to the individual: it is the expiry date of their pre-settled status. So late applicants can be those who fail to meet the deadline of 30 June 2021 to apply for initial status, but also those who miss their personal deadline to “upgrade” their status in the years to come. The guidance applies to this cohort of people.