There is no simple answer which will be more effective, it will depend on table size and data size to which you are going to update in one go.
Suppose you are using innodb engine and trying to update 1,000 or more rows in one go with 2 heavy tables join and it is quite frequent then it will not be good idea on production server as it will lock your table for some time and due to this locking some other operations also can be hit on your production server.
Option1: If you are trying to update few rows and based on proper indexed fields (preferred based on primary key) then you can go with join.
Option2: If you are trying to update a large amount of data based on multiple tables join then below option will be better:
Step1: Create a stored procedure.
Step2: Keep below query results in a cursor.
suppose you want TO UPDATE corresponding field2 DATA of TABLE table2 IN field1 of TABLE table1:
SELECT a.primary_key,b.field2 FROM table1 a JOIN table2 b ON a.primary_key=b.foreign_key WHERE [place CONDITION here IF any...];
Step3: Now update all rows one by one based on primary key using stored values in cursor.
Step4: You can call this stored procedure from your script.