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Have you read about the Wix Users API?
https://www.wix.com/corvid/reference/wix-users.html
https://www.wix.com/corvid/reference/wix-users-backend.html

If you look in the Wix Users Backend API you will see an approveByEmail or an approveByToken function there that you can use.
https://www.wix.com/corvid/reference/wix-users-backend.html#approveByEmail
https://www.wix.com/corvid/reference/wix-users-backend.html#approveByToken

Register a user sending an email for confirmation

This example demonstrates a common email verification flow. A user is initially registered but not yet approved. At registration, a verification email is sent with a link to a verification page. When a user goes to the verification page, the approval is granted and the user is logged into the site.

The code is split between three locations:

  • A backend web module named register.jsw .

  • The page code for the page where users register.

  • The page code for the page where users confirm their registration.

/*******************************
 * backend code - register.jsw *
 *******************************/
import wixUsersBackend from 'wix-users-backend';

export function doRegistration(email, password, firstName, lastName) {
  // register the user
  return wixUsersBackend.register(email, password, {
    "contactInfo": {
      "firstName": firstName,
      "lastName": lastName
    }
  } )
  .then( (results) => {
    // user is now registered and pending approval
    // send a registration verification email
    wixUsersBackend.emailUser('verifyRegistration', results.user.id, {
      "variables": {
        "name": firstName,
        "verifyLink": `http://yourdomain.com/post-register?token=${results.approvalToken}`
      }
    } );
  } );
}

export function doApproval(token) {
  // approve the user
  return wixUsersBackend.approveByToken(token)
  // user is now active, but not logged in
  // return the session token to log in the user client-side
    .then( (sessionToken) => {
      return {sessionToken, "approved": true};
    } )
    .catch( (error) => {
      return {"approved": false, "reason": error};
    } );
}

/*********************************
 * client-side registration code *
 *********************************/
import wixUsers from 'wix-users';
import {doRegistration} from 'backend/register';

export function button_click(event) {
  let email = // the user's email address
  let password = // the user's password
  let firstName = // the user's first name
  let lastName = // the user's last name

  doRegistration(email, password, firstName, lastName)
    .then( () => {
      console.log("Confirmation email sent.");
    } );
}

/**************************************
 * client-side post-registration code *
 **************************************/
import wixLocation from 'wix-location';
import wixUsers from 'wix-users';
import {doApproval} from 'backend/register';

$w.onReady( () => {
  // get the token from the URL
  let token = wixLocation.query.token;

  doApproval(token)
    .then( (result) => {
      if (result.approved){
        // log the user in
        wixUsers.applySessionToken(result.sessionToken);
          console.log("Approved");
      }
      else {
        console.log("Not approved!");
      }
    } );
} );