I finally found a way to fix the issue so I'm answering here.
I set the overflow-y on the #content instead, and wrapped my steps in another div. It works.
Here is the final code:
<body>
<div id="content">
<div id="steps">
<div class="step">this is the 1st step</div>
<div class="step">this is the 2nd step</div>
<div class="step">this is the 3rd step</div>
</div>
</div>
</body>
#content {
position:absolute;
width:100%;
overflow-y:hidden;
top:0;
bottom:0;
}
.step {
position:relative;
height:500px;
margin-bottom:500px;
}