diff --git a/mmvec/q2/_method.py b/mmvec/q2/_method.py
index d71ee31..515f4ca 100644
--- a/mmvec/q2/_method.py
+++ b/mmvec/q2/_method.py
@@ -75,7 +75,9 @@ def paired_omics(microbes: biom.Table,
         ranks = ranks - ranks.mean(axis=1).values.reshape(-1, 1)
         ranks = ranks - ranks.mean(axis=0)
         u, s, v = svds(ranks, k=latent_dim)
-
+        s = s[::-1]
+        u = u[:, ::-1]
+        v = v[::-1, :]
         microbe_embed = u @ np.diag(s)
         metabolite_embed = v.T
 
diff --git a/mmvec/q2/tests/test_method.py b/mmvec/q2/tests/test_method.py
index 6a4ef9f..0ce833b 100644
--- a/mmvec/q2/tests/test_method.py
+++ b/mmvec/q2/tests/test_method.py
@@ -59,6 +59,12 @@ def test_fit(self):
             res_biplot.features.shape,
             np.array([self.metabolites.shape[0], latent_dim]))
 
+        # make sure that the biplot has the correct ordering
+        self.assertGreater(res_biplot.proportion_explained[0],
+                           res_biplot.proportion_explained[1])
+        self.assertGreater(res_biplot.eigvals[0],
+                           res_biplot.eigvals[1])
+
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/scripts/mmvec b/scripts/mmvec
index 80b744c..1164c6d 100644
--- a/scripts/mmvec
+++ b/scripts/mmvec
@@ -198,6 +198,9 @@ def paired_omics(microbe_file, metabolite_file,
         # Save to an ordination file
         ranks = ranks - ranks.mean(axis=0)
         u, s, v = svds(ranks, k=latent_dim)
+        s = s[::-1]
+        u = u[:, ::-1]
+        v = v[::-1, :]
         microbe_embed = u @ np.diag(s)
         metabolite_embed = v.T
         pc_ids = ['PC%d' % i for i in range(microbe_embed.shape[1])]