You can use a Management Certificate contained in your Publish Settings file and 'bake' it yourself
Import-AzurePublishSettingsFile –PublishSettingsFile C:\Store\my.publishsettings
If you already have a certificate for management, you can store it in your vm and use it in PS
# Get management certificate from personal store
$certificate = Get-Item cert:\\CurrentUser\My\$CertificateThumbprint
if ($certificate -eq $null) {
throw “Management certificate for $SubscriptionName was not found in the users personal certificate store. Check thumbprint or install certificate”
}
# Set subscription profile
Set-AzureSubscription -SubscriptionName $SubscriptionName -SubscriptionId $SubscriptionId -Certificate $certificate
# Select subscription as the current context
Select-AzureSubscription -SubscriptionName $SubscriptionName