Chartjs-Chart.js with dual axis incorrect starting points (if negative values)

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Have you tried setting the same min value for both axes?

You can use ticks for specifying it:

ticks: {
          min: -5
        }

Here’s an example snippet I made for you:

var ctx = document.getElementById("myChart").getContext('2d');
var myChart = new Chart(ctx, {
  type: 'bar',
  data: {
    labels: ["Red", "Blue", "Yellow", "Green", "Purple", "Orange"],
    datasets: [{
      label: '# of Votes',
      data: [12, -5, 3, 5, 2, -3],
      backgroundColor: [
        'rgba(255, 99, 132, 0.2)',
        'rgba(54, 162, 235, 0.2)',
        'rgba(255, 206, 86, 0.2)',
        'rgba(75, 192, 192, 0.2)',
        'rgba(153, 102, 255, 0.2)',
        'rgba(255, 159, 64, 0.2)'
      ],
      borderColor: [
        'rgba(255,99,132,1)',
        'rgba(54, 162, 235, 1)',
        'rgba(255, 206, 86, 1)',
        'rgba(75, 192, 192, 1)',
        'rgba(153, 102, 255, 1)',
        'rgba(255, 159, 64, 1)'
      ],
      borderWidth: 1
    }]
  },
  options: {
    scales: {
      yAxes: [{
        position: "left",
        id: "y-axis-0",
        fontColor: '#fff',
        ticks: {
          min: -5
        }
      }, {
        position: "right",
        id: "y-axis-1",
        fontColor: '#fff',
        ticks: {
          min: -5
        }
      }]
    }
  }
});
<script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.4.0/Chart.bundle.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<div style="width:50%;">
  <canvas id="myChart" width="400" height="400"></canvas>
</div>

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