A sworn affidavit will no longer be proof that one is married under customary laws.
This follows the commencement of regulations published by the Attorney General in June.
The law, which came to effect on Tuesday, requires that all traditional marriages be registered.
Patrick Masiga, a marriage expert, said the law will protect children and women who are vulnerable when unions fail.
The marriage certificate, which can also be acquired at Huduma centers, is issued after 21 days of registration.
AG Githu Muigai ordered the registration of all customary marriages from August 1.
"All parties married under African customary law are required to register their marriages," the AG said in a June 9 Gazette notice.
The registration takes place at Sheria House ground floor, and is in line with Marriage (Customary Marriage) Rules, 2017, and stipulations of Section 96 of Marriage Act, 2014.
Parties who wish to contract customary marriage from the above date must obtain prior authorisation from the registrar.
"Parties to a customary marriage shall notify the Registrar of such marriage within three months of completion of the relevant ceremonies or steps required to confer the status of marriage to the parties in the community concerned," says Marriage Act 2014.
Certificates will only be issued to people whose applications are successful.
The requirements were meant to make both partners, in marriages solemnised by the two methods, eligible for equal share of property in the event they divorce. Women were seen as the biggest winners.