If you can decode JWT, how are they secure

The correct way to avoid SQL injection attacks, no matter which database you use, is to separate the data from SQL, so that data stays data and will never be interpreted as commands by the SQL parser. It is possible to create SQL statement with correctly formatted data parts, but if you don't fully understand the details, you should always use prepared statements and parameterized queries. These are SQL statements that are sent to and parsed by the database server separately from any parameters. This way it is impossible for an attacker to inject malicious SQL.

You basically have two options to achieve this:

1. Using PDO (for any supported database driver):

    $stmt = $pdo->prepare('SELECT * FROM employees WHERE name = :name');
   
    $stmt->execute([ 'name' => $name ]);
   
    foreach ($stmt as $row) {
        // Do something with $row
    }
   

2. Using MySQLi (for MySQL):

    $stmt = $dbConnection->prepare('SELECT * FROM employees WHERE name = ?');
    $stmt->bind_param('s', $name); // 's' specifies the variable type => 'string'
   
    $stmt->execute();
   
    $result = $stmt->get_result();
    while ($row = $result->fetch_assoc()) {
        // Do something with $row
    }
   

If you're connecting to a database other than MySQL, there is a driver-specific second option that you can refer to (for example, pg_prepare() and pg_execute() for PostgreSQL). PDO is the universal option.

Correctly setting up the connection

Note that when using PDO to access a MySQL database real prepared statements are not used by default. To fix this you have to disable the emulation of prepared statements. An example of creating a connection using PDO is:

$dbConnection = new PDO('mysql:dbname=dbtest;host=127.0.0.1;charset=utf8', 'user', 'password');

$dbConnection->setAttribute(PDO::ATTR_EMULATE_PREPARES, false);
$dbConnection->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);

In the above example the error mode isn't strictly necessary, but it is advised to add it. This way the script will not stop with a Fatal Error when something goes wrong. And it gives the developer the chance to catch any error(s) which are thrown as PDOExceptions.

What is mandatory, however, is the first setAttribute() line, which tells PDO to disable emulated prepared statements and use real prepared statements. This makes sure the statement and the values aren't parsed by PHP before sending it to the MySQL server (giving a possible attacker no chance to inject malicious SQL).

Although you can set the charset in the options of the constructor, it's important to note that 'older' versions of PHP (before 5.3.6) silently ignored the charset parameter in the DSN.

Explanation

The SQL statement you pass to prepare is parsed and compiled by the database server. By specifying parameters (either a ? or a named parameter like :name in the example above) you tell the database engine where you want to filter on. Then when you call execute, the prepared statement is combined with the parameter values you specify.

The important thing here is that the parameter values are combined with the compiled statement, not an SQL string. SQL injection works by tricking the script into including malicious strings when it creates SQL to send to the database. So by sending the actual SQL separately from the parameters, you limit the risk of ending up with something you didn't intend.

Any parameters you send when using a prepared statement will just be treated as strings (although the database engine may do some optimization so parameters may end up as numbers too, of course). In the example above, if the $name variable contains 'Sarah'; DELETE FROM employees the result would simply be a search for the string "'Sarah'; DELETE FROM employees", and you will not end up with an empty table.

Another benefit of using prepared statements is that if you execute the same statement many times in the same session it will only be parsed and compiled once, giving you some speed gains.

Oh, and since you asked about how to do it for an insert, here's an example (using PDO):

$preparedStatement = $db->prepare('INSERT INTO table (column) VALUES (:column)');

$preparedStatement->execute([ 'column' => $unsafeValue ]);

Can prepared statements be used for dynamic queries?

While you can still use prepared statements for the query parameters, the structure of the dynamic query itself cannot be parametrized and certain query features cannot be parametrized.

For these specific scenarios, the best thing to do is use a whitelist filter that restricts the possible values.

// Value whitelist
// $dir can only be 'DESC', otherwise it will be 'ASC'
if (empty($dir) || $dir !== 'DESC') {
   $dir = 'ASC';
}

How about taking another approach or angle at this problem? Ask why the password is required to be in plaintext: if it's so that the user can retrieve the password, then strictly speaking you don't really need to retrieve the password they set (they don't remember what it is anyway), you need to be able to give them a password they can use.

Think about it: if the user needs to retrieve the password, it's because they've forgotten it. In which case a new password is just as good as the old one. But, one of the drawbacks of common password reset mechanisms used today is that the generated passwords produced in a reset operation are generally a bunch of random characters, so they're difficult for the user to simply type in correctly unless they copy-n-paste. That can be a problem for less savvy computer users.

One way around that problem is to provide auto-generated passwords that are more or less natural language text. While natural language strings might not have the entropy that a string of random characters of the same length has, there's nothing that says your auto-generated password needs to have only 8 (or 10 or 12) characters. Get a high-entropy auto-generated passphrase by stringing together several random words (leave a space between them, so they're still recognizable and typeable by anyone who can read). Six random words of varying length are probably easier to type correctly and with confidence than 10 random characters, and they can have a higher entropy as well. For example, the entropy of a 10 character password drawn randomly from uppercase, lowercase, digits and 10 punctuation symbols (for a total of 72 valid symbols) would have an entropy of 61.7 bits. Using a dictionary of 7776 words (as Diceware uses) which could be randomly selected for a six word passphrase, the passphrase would have an entropy of 77.4 bits. See the Diceware FAQ for more info.

• a passphrase with about 77 bits of entropy: "admit prose flare table acute flair"

• a password with about 74 bits of entropy: "K:&$R^tt~qkD"

I know I'd prefer typing the phrase, and with copy-n-paste, the phrase is no less easy to use that the password either, so no loss there. Of course if your website (or whatever the protected asset is) doesn't need 77 bits of entropy for an auto-generated passphrase, generate fewer words (which I'm sure your users would appreciate).

I understand the arguments that there are password protected assets that really don't have a high level of value, so the breach of a password might not be the end of the world. For example, I probably wouldn't care if 80% of the passwords I use on various websites was breached: all that could happen is a someone spamming or posting under my name for a while. That wouldn't be great, but it's not like they'd be breaking into my bank account. However, given the fact that many people use the same password for their web forum sites as they do for their bank accounts (and probably national security databases), I think it would be best to handle even those 'low-value' passwords as non-recoverable.