Setting the color of all checkboxes in their active state is a bit more involved than you might have expected originally. That's because the specificity of your custom css must match or exceed that of the Bootstrap rules.
Below you'll find a working code snippet with the required custom css overrides. And you'll notice that it only changes the color of the buttons (as you requested) and does not change the color of the glow when a button is in focus.
Click the "run code snippet" button below to test this out:
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
<style>
.btn-warning:not(:disabled):not(.disabled).active,
.btn-warning:not(:disabled):not(.disabled):active,
.show>.btn-warning.dropdown-toggle {
background-color: limegreen;
border-color: limegreen;
}
.btn-success:not(:disabled):not(.disabled).active,
.btn-success:not(:disabled):not(.disabled):active,
.show>.btn-success.dropdown-toggle {
background-color: limegreen;
border-color: limegreen;
}
.btn-danger:not(:disabled):not(.disabled).active,
.btn-danger:not(:disabled):not(.disabled):active,
.show>.btn-danger.dropdown-toggle {
background-color: limegreen;
border-color: limegreen;
}
</style>
<div class="btn-group btn-group-toggle m-3" data-toggle="buttons">
<label class="btn btn-success">
<input type="checkbox" name="option1" id="option1" autocomplete="off" checked> Low
</label>
<label class="btn btn-warning">
<input type="checkbox" name="option2" id="option2" autocomplete="off"> Medium
</label>
<label class="btn btn-danger">
<input type="checkbox" name="option3" id="option3" autocomplete="off"> High
</label>
</div>