Always Encrypted in Entity Framework Core Support

Do not role your own implementation. What we ended up doing was creating a separate Windows Classic Desktop class library project in our solution that handled the data layer for the table with encrypted columns. We used Dapper for the ORM in that project and it supported the encrypted columns. It really limited some things we could do since the rest of our data layer was through EF Core but it works.

Since you are using Azure SQL, I would also recommend using the Microsoft Azure Key Vault to store the column master key. See the NuGet package Microsoft.SqlServer.Management.AlwaysEncrypted.AzureKeyVaultProvider. This NuGet package is also not supported in .NET Core.