Multi-Factor Authentication has become a requirement for any application that values security. In fact, it has become a regulatory requirement in some industries and is being adopted as a requirement in several others. We often discover misconceptions or downright misunderstandings about how MFA works and think this is a topic worth diving into. This particular article will focus on one of the most common second factors, Time based One Time Password, or TOTP.

Introduction to TOTP

TOTP authentication uses a combination of a secret and the current time to derive a predictable multi-digit value. The secret is shared between the issuer and the user in order to compare generated values to determine if the user in fact posses the required secret. You may have heard this incorrectly referred to as “Google Authenticator”. While Google had a major part in popularizing this method, it has nothing to do with how TOTP actually works. Any site may create and issue tokens and any mobile application with a correct implementation of TOTP generation may produce a one time value. In this article we will implement server side TOTP token issuing and discuss its security requirements.

To read more about TOTP token generation, please take a look at RFC 6238.

The example code in this article is written in Java. This task can be accomplished in any programming language that supports the underlying cryptographic functions.

Establishing a Seed

The foundation for the security of a TOTP token begins with the seed. This value is used in conjunction with the current time to derive the instance of the token. Because time can be calculated it is not suitable as the only value for our token. Choosing a seed is incredibly important and should not be left up to the user. Seeds should be randomly generated using a Cryptographically Secure Pseudo Random Number Generator. You can determine the number of bytes you want to use, and in this example we are using 64. We will use the SecureRandom implementation provided by the Java language.

static String generateSeed() {
    SecureRandom random = new SecureRandom();
    byte[] randomBytes = new byte[SEED_LENGTH_IN_BYTES];
    return printHexBinary(randomBytes);

In order to cosume the token we will return the hex representation of the bytes generated. This allows us to pass the value around a bit easier.

Establishing a counter

The other side of TOTP token generation relies on the current time. We take the current time represented as a long, which is the number of seconds since epoch. This can be derived using System.currentTimeMillis() / 1000L. Next, we take the value and divide it by our period, or the number of seconds the token will be valid before rotating. We will use a value of 30 in our example, which is the recommended setting. Finally, we need to put the value into a byte array. There are a few ways to do this, but the following method is on the conservative side accounting for non 64 bit longs and possible endian differences.

private static byte[] counterToBytes(long time) {
    long counter = time / PERIOD;
    buffer = new byte[Long.SIZE / Byte.SIZE];
    for (int i = 7; i >= 0; i--) {
        buffer[i] = (byte)(counter & 0xff);
        counter = counter >> 8;
    return buffer;

Once we have this value we can execute our hmac operation to produce the long form of our OTP value.

Generating a Value

Using the seed as a key and the counter as a message, we will derive our long form OTP value. The value returned from our HMac operation will be truncated in order to produce the 6 digit value we will compare against in the end. The following code is an HMacSHA1 operation using the standard Java encryption libraries. While RFC 6238 describes the possible options of HMacSHA256 and HMacSHA512, they are not viable when distributing the secret for use on most mobile authenticator applications.

private static byte[] hash(final byte[] key, final byte[] message) {
    try {
        Mac hmac = Mac.getInstance("HmacSHA1");
        SecretKeySpec keySpec = new SecretKeySpec(key, "RAW");
        return hmac.doFinal(message);
    } catch (NoSuchAlgorithmException | InvalidKeyException e) {
        log.error(e.getMessage(), e);
        return null;

With the ability to hash our seed and message we can now derive our TOTP value:

static String generateInstance(final String seed, final byte[] counter) {
    byte[] key = hexToBytes(seed);
    byte[] result = hash(key, counter);

    if (result == null) {
        throw new RuntimeException("Could not produce OTP value");

    int offset = result[result.length - 1] & 0xf;
    int binary = ((result[offset]     & 0x7f) << 24) |
                 ((result[offset + 1] & 0xff) << 16) |
                 ((result[offset + 2] & 0xff) << 8)  |
                 ((result[offset + 3] & 0xff));

    StringBuilder code = new StringBuilder(Integer.toString(binary % POWER));
    while (code.length() < DIGITS) code.insert(0, "0");
    return code.toString();

Using the seed as the key and the counter as the message, we perform the necessary conversions, perform the hash, and truncate the message according to the specification. Finally, we divide the result by 10 to the power of the expected digits (in our case 6) and convert that to a string value. If the result is less than 6 digits we pad it with zeros.

Providing the Secret to the User

In order to provide the secret to the user, we need to provide a consistent string in a format that allows the user to generate tokens reliably. There are several ways to do this, including simply providing the secret and issuer to the user directly. The most common method is by providing a QR code that contains the information. For this example we will use the Zebra Crossing library.

class QrCode {
    private static final int WIDTH = 350;
    private static final int HEIGHT = 350;

    static void generate(String applicationName, String issuer, String path, String secret) {
        try {
            String qrdata = String.format("otpauth://totp/%s?secret=%s&issuer=%s", applicationName, secret, issuer);
            generateQRCodeImage(qrdata, path);
        } catch (WriterException | IOException e) {
            System.out.println("Could not generate QR Code: " + e.getMessage());

    private static void generateQRCodeImage(String text, String filePath) throws WriterException, IOException {
        QRCodeWriter qrCodeWriter = new QRCodeWriter();
        BitMatrix bitMatrix = qrCodeWriter.encode(text, BarcodeFormat.QR_CODE, WIDTH, HEIGHT);
        Path path = FileSystems.getDefault().getPath(filePath);
        MatrixToImageWriter.writeToPath(bitMatrix, "PNG", path);

Executing this code will save a PNG with the corresponding QR code. In a real world situation, you would render this image directly to the user for import by their application of choice.

Consuming the Token

In order to test our implementation we will need a program that can accept an otpauth:// string or a QR Code. This can be done a number of ways. If you want to do this via a mobile device, you can use Google Authenticator or Authy. Both of these programs will scan a QR code. If you want to try locally, 1Password provides a way to import a QR image by adding a label to a login and selecting One-Time Password as the type. You can import the created image using the QR code icon and selecting the path to the generated image. Once the secret is imported it will start producing values. You can use these as your entry values into the example program.

Protecting the Seed

It is important to respect the secret for what it is — a secret. With any secret we must do our part to protect it from misuse. How do we do this? Like any other piece of persisted sensitive information, we encrypt it. Because these secrets are not large in size, we have a number of options at our disposal. The important part is not to manage this step on your own. Take advantage of a system that can encrypt and decrypt for you and just worry about storing the encrypted secret value. There are cloud based tools like Amazon KMS, Google Cloud Key Management, and Azure Key Vault as well as services you can run like Thycotic Secret Server, CyberArk Conjur, and Hashicorp Vault. All of these options require some kind of setup, and some are commercial products.

Setting up Secret Storage

To keep this example both relevant and free of cost to run, we will use Hashicorp Vault. Vault is an open source project with an optional enterprise offering. It’s a wonderful project with capabilities far past this example. There are a number of ways to install Vault, but since it is a single binary, the easiest way is to download the binary and run it. Start vault with the development flag:

λ vault server -dev

During the boot sequence you will be presented with an unseal key and a root token. The example program will expect the VAULT_TOKEN environment variable to be set to the root token provided. Your output will be similar to the following:

λ vault server -dev ==> Vault server configuration:

Api Address:
Cgo: disabled
Cluster Address:
Listener 1: tcp (addr: "", cluster address: "", max_request_duration: "1m30s", max_request_size: "33554432", tls: "disabled")
Log Level: (not set)
Mlock: supported: false, enabled: false
Storage: inmem
Version: Vault v0.11.2
Version Sha: 2b1a4304374712953ff606c6a925bbe90a4e85dd

WARNING! dev mode is enabled! In this mode, Vault runs entirely in-memory
and starts unsealed with a single unseal key. The root token is already
authenticated to the CLI, so you can immediately begin using Vault.

You may need to set the following environment variable:


The unseal key and root token are displayed below in case you want to
seal/unseal the Vault or re-authenticate.

Unseal Key: mkniY94IlJngQz07gfPZlQnZnvEHMXWQ3/MiFegsfr8=
Root Token: 4uYnD1vVZZcNkbYe03t0cLkh

Development mode should NOT be used in production installations!

Once Vault is booted you will need to enable the Transit Backend. This allows us to create an encryption key inside of Vault and seamlessly encrypt and decrypt information.

λ export VAULT_ADDR=
λ vault secrets enable transit
Success! Enabled the transit secrets engine at: transit/

λ vault write -f transit/keys/how_it_works_totp
Success! Data written to: transit/keys/how_it_works_totp

λ echo "my secret" | base64

λ vault write transit/encrypt/myapp plaintext=Im15IHNlY3JldCIgDQo=
Key Value
--- -----
ciphertext vault:v1:/HeILzBTv+JbxdaYeKLVB9RVH9o/b+Lilrja88VhCuaSSlvUY+IzHp2Uλ vault write transit/encrypt/myapp plaintext=Im15IHNlY3JldCIgDQo=

λ vault write -field=plaintext transit/decrypt/myapp ciphertext=vault:v1:/HeILzBTv+JbxdaYeKLVB9RVH9o/b+Lilrja88VhCuaSSlvUY+IzHp2U | base64 -d
"my secret"

We can now encrypt and decrypt our TOTP secrets. The only thing left is to persist those secrets so that they can be referenced on login. For this example we will not be creating a complete user system, but we will setup a database and create an entry with an encrypted seed value to show what the end to end process will resemble.

To encrypt and decrypt our seed we can use a Vault library. The following example demonstrates the essential pieces:

String encryptSeed(String seed) throws VaultException {
    final Map<String, Object> entry = new HashMap<>();
    entry.put("plaintext", seed);
    final LogicalResponse response = client.logical().write("transit/encrypt/myapp", entry);
    return response.getData().get("ciphertext");

String decryptSeed(String ciphertext) throws VaultException {
    final Map<String, Object> entry = new HashMap<>();
    entry.put("ciphertext", ciphertext);
    final LogicalResponse response = client.logical().write("transit/decrypt/myapp", entry);
    return response.getData().get("plaintext");

Note the lack of error handling. In a production system you would want to handle the negative and null cases appropriately.

Finally, we take the output of the vault encryption operation and store it in our database. The sample code contains database handling logic, but it is typical boilerplate database code an not directly relevant to explaining the design of a TOTP system.


By now it should be pretty obvious that time synchronization is of the utmost importance. If the server and client differ more than the period, the token comparison will fail. The RFC describes methods for determining drift and tolerance for devices that have drifted for too many periods. This example does not address drift or resynchronization, but it is recommended that a production implementation address this issue.

Running the Example

The source code for this example is available on Github. Make sure you have read an executed all of the steps above before attempting to run the example. Additionally, you will need to have PostgreSQL installed and running. If this is your first time running the example, you will need to be sure to import the generated token using your preferred application before attempting to type in a value. You should have your MFA token generator application open and the test token selected. You can setup and execute the program by running:

createdb totp
mvn flyway:migrate
mvn compile
# For Unix users
# For Windows users
mvn -q exec:java -Dexec.mainClass=com.jemurai.howitworks.totp.Main

You will be prompted to enter your token value. After pressing return the program will echo the value you entered, the expected token value, and if the values match. This is the core logic necessary to confirm a TOTP based MFA authentication sequence. If your token values do not match, make sure to enter your token value with plenty of time to spare on the countdown. Because we have not implemented a solution that accounts for drift, the value must be entered during the same period the server generates the expected value. If this is your first time running the example you will need to import the QR code that was generated before the input prompt. If everything was done correctly you will see output similar to the following:

MFA Token:
Entered: 808973 : Generated: 808973 : Match: true

At this point you have successfully implemented server side TOTP based MFA and used a client side token generator to validate the implementation.

Security Pitfalls of TOTP

For a long time TOTP or really, just OTP based MFA was the best option. It was popularized by RSA long before smart phones were capable of generating tokens. This method is fundamentally secure but is open to human error. Well crafted phishing attacks can obtain and replay TOTP based MFA responses. Several years ago FIDO and U2F were introduced and this is now the “most secure” option available. It comes with benefits and drawbacks and like all solutions should be carefully considered before use.


Multi-Factor Authentication is an important part of the security of your information systems. Any system providing access to sensitive information should employ the use of MFA to protect that information. With credential theft via phishing on the rise, this could be one of the most important controls you establish. While this article examines an implementation of TOTP token based MFA, you should seek an established provider like Okta, OneLogin, Duo, Auth0, etc. to provide a production ready solution.

Aaron Bedra

Aaron was formerly Jemurai's Chief Scientist and currently acts as an Advisor.