Set Availability Zones in a VPC for Elastic Beanstalk Instances with Custom Settings
The "Custom Availability Zones" option can only be specified for Elastic Beanstalk environments that don't use custom VPC settings.
You can work around this issue by configuring your instances to run in a particular subnet or subnets. Each subnet is associated with a single Availability Zone. Therefore, you can indirectly implement custom Availability Zones by configuring your instance to run in a subnet or subnets created in a designated Availability Zone.
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Set Availability Zones in a VPC for Elastic Beanstalk Instances with Custom Settings
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