Are there any benefits to using vulnerability scanners such as Nessus Pro or Tenable.io, if we are already using Azure Security Center for vulnerability and update management?
Or does it have any negative effects to do so?
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Azure Security Center rather identifies insecure configurations (e.g. missing system updates) than concrete vulnerabilities. While Nessus authenticated scans also cover insecure configurations, they additionally discovers vulnerable installed software (e.g. through CVE matching).
I dont think that the Azure Security Center sees itself as vulnerability assessment solution. Nessus definitely does that. I would say if you have moderate to high security requirements you should use both.