I followed this https://confluence.atlassian.com/adminjiraserver/create-edit-or-remove-a-user-938847025.html
however I don't see an "active" checkbox in the user profile page.
Are you on Server Version 8.1?
If you have script runner add-on installed, use the below script to deactivate the users,
import com.atlassian.jira.component.ComponentAccessorimport com.atlassian.crowd.embedded.api.CrowdServiceimport com.atlassian.crowd.embedded.api.UserWithAttributes
import org.apache.log4j.Levellog.setLevel(Level.INFO)
def numOfDays = 90 as intdef dateLimit = ( new Date() ) - numOfDays
def groupManager = ComponentAccessor.groupManagerdef crowdService = ComponentAccessor.crowdServicedef userManager = ComponentAccessor.userManagerdef userUtil = ComponentAccessor.userUtil
def const_groupname = 'jira-users'def group = groupManager.getGroup(const_groupname)def groupMembers = groupManager.getDirectUsersInGroup(group)
def counter = 0 as intgroupMembers.each{ applicationUser ->if( applicationUser.isActive() ){def user = crowdService.getUserWithAttributes( applicationUser.name ) as UserWithAttributesdef lastLoginMillis = user.getValue('login.lastLoginMillis') as Stringif( lastLoginMillis?.isNumber() ){def date = new Date(Long.parseLong(lastLoginMillis)) as Dateif( date.before(dateLimit) ){counter++userUtil.removeUserFromGroup(group, applicationUser)}}}}
log.info "Removed ${counter} users"
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