Disclosed are various approaches for integrating application scanning into a mobile enterprise computing management system. A management service can add a first command to a command queue associated with a client device, wherein the first command instructs the client device to provide a unique device identifier associated with the client device to the management service and the unique device identifier uniquely identifies the client device with respect to at least one other client device. Then, the management service can receive a first request from the client device for the first command stored in the command queue. Later, the management service sends the first command to the client device. When the management service receives the unique device identifier from the client device, the management service sends the unique device identifier to a scanning service and a policy linked with the unique device identifier to the scanning service. The policy comprises an identifier of a client application prohibited on the client device. The management service then receives a notification from the scanning service. The notification comprises the unique device identifier and an indication that the client application is present on the client device. Later, the management service adds a second command to the command queue, wherein the second command instructs the client device to perform a remedial action specified by the policy. When the management service receives a second request from the client device for the second command stored in the command queue, the management service sends the second command to the client device.