How to setup bastion hosts for accessing EC2 instances that are in different VPCs

Hi, you can use a single bastion host to access all your EC2 instances anywhere they reside as long as there is a connectivity between the bastion host and the instances that you're trying to reach. There are several ways that you can use to connect VPCs together such as VPC-Peering, Transit Gateway, site-to-site VPNs, etc..

I would recommend using AWS System Manager as a way to access your EC2 instances no matter where they reside instead of using a bastion host.

You can read a bit about it here:

https://docs.aws.amazon.com/systems-manager/latest/userguide/session-manager.html

if you just need CLI access then better to use cloudshell than bastion hosts.

But yes, VPC peering / TGW can be used to access other VPC from a single bastion host as long connectivity/ACL permits.

https://aws.amazon.com/blogs/aws/aws-cloudshell-command-line-access-to-aws-resources/