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Assuming routing and everything else is setup properly I would suggest enabling VPC Flow logs with additional Meta-Data to find out what is being rejected in both the Source and Destination VPCs.
https://aws.amazon.com/blogs/aws/learn-from-your-vpc-flow-logs-with-additional-meta-data/
Knowledge center article for troubleshooting connectivity over VPC Peering.
https://aws.amazon.com/premiumsupport/knowledge-center/vpc-peering-connectivity/
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I have added flow logs and it seems that none of the traffic goes through the VPC (I'm guessing this is the case since the logs seem very empty, don't show any source or destination IP or anything). Is it possible for the lambda that is connected to the VPC to not send traffic through it?
Best way for you to isolate this is to create vanilla EC2 instance in the Source VPC and in the destination VPC and test a simple connectivity such as SSH over the Peering if that works fine then it is something with the Lambda or MongoDB that needs fixed.