You can keep track of the 2 min values in your for loop. You will also need to keep track of the ids that correspond to those min values. You can see a working snippet here below:

var passengers = document.querySelectorAll(".car");
var trainCar = {};

let min = Infinity;
let min2 = Infinity;
let minId, min2Id;

for (let i = 0; i <= passengers.length-1; i++) {
    const value = Math.floor(Math.random() * 100); 
    if(value < min){
      min2 = min;
      min2Id = minId;
      min = value;
      minId = i;
    } else if (value < min2){
      min2 = value;
      min2Id = i;
    }
    passengers[i].innerHTML = value;
    trainCar[i] = {
        numberOfPassengers: value,
        carId: passengers[i].id,
    }
}

passengers[minId].style.backgroundColor = 'grey';
passengers[min2Id].style.backgroundColor = 'grey';

<div class="train">
    <div class="car" id = "car1">a</div>
    <div class="car" id = "car2">b</div>
    <div class="car" id = "car3">b</div>
    <div class="car" id = "car4">b</div>
    <div class="car" id = "car5">b</div>
    <div class="car" id = "car6">b</div>
</div>

First of all, I apologize if this is a stupid question, I’m fairly new to JavaScript and have been experimenting and trying to do this for several days now.

Let’s say I have 6 train cars (divs) with their respective id’s.

<div class="train">
    <div class="car" id = "car1">a</div>
    <div class="car" id = "car2">b</div>
    <div class="car" id = "car3">b</div>
    <div class="car" id = "car4">b</div>
    <div class="car" id = "car5">b</div>
    <div class="car" id = "car6">b</div>
</div>

My script generates innerText of these divs using random numbers from 0 to 160 (number of passengers in each respective train car).
I want to change the background color of 2 cars with the least amount of passengers.

First, I create a new Object of trainCar to contain information about the number of passengers and the car id.

var passengers = document.querySelectorAll(".car");
var trainCar = {};

for (let i = 0; i <= passengers.length-1; i++) {
    passengers[i].innerHTML = getRandomNumber(); 
    trainCar[i] = {
        numberOfPassengers: passengers[i].innerHTML,
        carId: passengers[i].id,
    }
}

This creates multiple objects within my main object trainCar (this is the console.log):

{0: {…}, 1: {…}, 2: {…}, 3: {…}, 4: {…}, 5: {…}}
0: {numberOfPassengers: "17", carId: "car1"}
1: {numberOfPassengers: "87", carId: "car2"}
2: {numberOfPassengers: "106", carId: "car3"}
3: {numberOfPassengers: "157", carId: "car4"}
4: {numberOfPassengers: "154", carId: "car5"}
5: {numberOfPassengers: "56", carId: "car6"}

So this is where I’m stuck. I can change background color of one of the cars using:
document.getElementById(trainCar[2].carId).style="background-color: grey";
but I have no idea how to match the lowest value of innerHTML with the corresponding id and change this id’s background (let alone the lowest two).