Just checking in is a standard phrase used to start an email (or other message) that’s intended to ask someone for a response or follow-up action in a friendly, informal way. However, it’s a cliché opening that can come across as passive-aggressive, so we recommend avoiding it in favor of a more direct opening like “We previously discussed …”
In a more personal context, you might encounter “just checking in” as part of a longer phrase such as “I’m just checking in to see how you’re doing”. In this case, it’s not asking the other person to do anything but rather asking about their well-being (emotional or physical) in a friendly way.