The answer is yes.
With the Windows Update settings set to "Check for Updates but let me choose whether to download and install them", you may set the Windows Defender settings to check for new definitions before a "Windows Defender Scheduled Scan".
To automatically check for new definitions before Windows Defender scheduled scans (recommended):
Click to open Windows Defender by going to Control Panel > Windows Defender
Click Tools, and then click Options.
Under Automatic scanning, make sure the "Automatically scan my computer (recommended)" check box is selected.
Select the "Check for updated definitions before scanning" check box, and then click Save. If you are prompted for an administrator password or confirmation, type the password or provide confirmation.
Source: Microsoft Support
Simple answer: "C:\program files\windows defender\mpcmdrun.exe" -scan -scantype 2
Elaborated:
1) Open a simple (not elevated) command prompt.
It should not be necessary to open an elevated one.
2) Type/copy--> "C:\program files\windows defender\mpcmdrun.exe" -scan -scantype 2
C:\program files\windows defender\mpcmdrun.exe should be the deafult location of mpcmdrun.exe
Using only -scan parameter will use the default settings of Windows defender/essentials
To be certain that it will be performed a full system scan, you need to use the -scantype 2 parameter, like said in the mpcmdrun help.
3) If you have errors, first try to locate where it is the mpcmdrun.exe file on your machine.
This is usually and easily done with a simple search:
From command prompt: dir /a /b /s c:\mpcmdrun.exe
From the run window, shortcut: Windows key + R key (Windows + R), or from Windows vista/7 searchbox (right over the start button, after you have clicked it), or from Windows 8/8.1 charm search, or from Windows 8/8.1 - right-click on the start button - run:
cmd /k dir /a /b /s c:\mpcmdrun.exe
Extracted from the mpcmdrun help:
-Scan [-ScanType #] [-File <path> [-DisableRemediation]] Scans for malicious software
-Scan [-ScanType value]
0 Default, according to your configuration
1 Quick scan
2 Full system scan
3 File and directory custom scan
[-File <path>]
Indicates the file or directory to be scanned, only valid for custom scan.
Best Answer
There's a lot of threads to find in Google about this subject. It doesn't seem like Microsoft is willing to document this, but many people have just done it and I don't see any complaints. Should be safe enough.
If you want to be sure, just create a restore point, move all files to a temporary folder, reboot machine, update Windows and Windows Defender, reboot again and see if:
Good luck.