It's simply setting an app setting called XDT_MicrosoftApplicationInsights_Mode with value recommended (to enable) or default (to disable) as described here. You can do that both in ARM or PowerShell as below.
ARM (check appSettings part):
{
"resources": [
{
"name": "[parameters('name')]",
"type": "Microsoft.Web/sites",
"properties": {
"siteConfig": {
"appSettings": [
{
"name": "APPINSIGHTS_INSTRUMENTATIONKEY",
"value": "[reference('microsoft.insights/components/AppMonitoredSite', '2015-05-01').InstrumentationKey]"
},
{
"name": "APPLICATIONINSIGHTS_CONNECTION_STRING",
"value": "[reference('microsoft.insights/components/AppMonitoredSite', '2015-05-01').ConnectionString]"
},
{
"name": "ApplicationInsightsAgent_EXTENSION_VERSION",
"value": "~2"
},
{
"name": "XDT_MicrosoftApplicationInsights_Mode ",
"value": "recommended"
}
]
},
"name": "[parameters('name')]",
"serverFarmId": "[concat('/subscriptions/', parameters('subscriptionId'),'/resourcegroups/', parameters('serverFarmResourceGroup'), '/providers/Microsoft.Web/serverfarms/', parameters('hostingPlanName'))]",
"hostingEnvironment": "[parameters('hostingEnvironment')]"
},
"dependsOn": [
"[concat('Microsoft.Web/serverfarms/', parameters('hostingPlanName'))]",
"microsoft.insights/components/AppMonitoredSite"
],
"apiVersion": "2016-03-01",
"location": "[parameters('location')]"
},
{
"apiVersion": "2016-09-01",
"name": "[parameters('hostingPlanName')]",
"type": "Microsoft.Web/serverfarms",
"location": "[parameters('location')]",
"properties": {
"name": "[parameters('hostingPlanName')]",
"workerSizeId": "[parameters('workerSize')]",
"numberOfWorkers": "1",
"hostingEnvironment": "[parameters('hostingEnvironment')]"
},
"sku": {
"Tier": "[parameters('sku')]",
"Name": "[parameters('skuCode')]"
}
},
{
"apiVersion": "2015-05-01",
"name": "AppMonitoredSite",
"type": "microsoft.insights/components",
"location": "West US 2",
"properties": {
"ApplicationId": "[parameters('name')]",
"Request_Source": "IbizaWebAppExtensionCreate"
}
}
],
"parameters": {
"name": {
"type": "string"
},
"hostingPlanName": {
"type": "string"
},
"hostingEnvironment": {
"type": "string"
},
"location": {
"type": "string"
},
"sku": {
"type": "string"
},
"skuCode": {
"type": "string"
},
"workerSize": {
"type": "string"
},
"serverFarmResourceGroup": {
"type": "string"
},
"subscriptionId": {
"type": "string"
}
},
"$schema": "https://schema.management.azure.com/schemas/2014-04-01-preview/deploymentTemplate.json#",
"contentVersion": "1.0.0.0"
}
Powershell:
$app = Get-AzWebApp -ResourceGroupName "AppMonitoredRG" -Name "AppMonitoredSite" -ErrorAction Stop
$newAppSettings = @{} # case-insensitive hash map
$app.SiteConfig.AppSettings | %{$newAppSettings[$_.Name] = $_.Value} # preserve non Application Insights application settings.
$newAppSettings["APPINSIGHTS_INSTRUMENTATIONKEY"] = "012345678-abcd-ef01-2345-6789abcd"; # set the Application Insights instrumentation key
$newAppSettings["APPLICATIONINSIGHTS_CONNECTION_STRING"] = "InstrumentationKey=012345678-abcd-ef01-2345-6789abcd"; # set the Application Insights connection string
$newAppSettings["ApplicationInsightsAgent_EXTENSION_VERSION"] = "~2"; # enable the ApplicationInsightsAgent
$newAppSettings["XDT_MicrosoftApplicationInsights_Mode"] = "recommended"; # set the APM collection to recommended
$app = Set-AzWebApp -AppSettings $newAppSettings -ResourceGroupNamrecommendede $app.ResourceGroup -Name $app.Name -ErrorAction Stop