EnableTransparentDataEncryption.ps1

<#
    .DESCRIPTION
        Enables Transparent Data Encryption on all Azure SQL Databases within a subscription
    .NOTES
        AUTHOR: @dazfuller
        LASTEDIT: Jan 12, 2017
#>

$connectionName = "AzureRunAsConnection"

try
{
    $servicePrincipalConnection = Get-AutomationConnection -Name $connectionName

    "Logging into Azure..."
    Login-AzureRmAccount `
        -ServicePrincipal `
        -TenantId $servicePrincipalConnection.TenantId `
        -ApplicationId $servicePrincipalConnection.ApplicationId `
        -CertificateThumbprint $servicePrincipalConnection.CertificateThumbprint
}
catch
{
    if (!$servicePrincipalConnection)
    {
        $errorMessage = "Connection $connectionName not found."
        throw $errorMessage
    }
    else
    {
        Write-Error -Message $_.Exception
        throw $_.Exception
    }
}

Get-AzureRmResourceGroup `
    | Get-AzureRmSqlServer `
    | Get-AzureRmSqlDatabase `
    | Where-Object -FilterScript { $_.DatabaseName -ne "master" } `
    | Get-AzureRmSqlDatabaseTransparentDataEncryption `
    | Where-Object -FilterScript { $_.State -ne "Enabled" } `
    | Set-AzureRmSqlDatabaseTransparentDataEncryption -State Enabled