diff --git a/ipyrad/analysis/pca.py b/ipyrad/analysis/pca.py
index 29608f72..2a858c9e 100644
--- a/ipyrad/analysis/pca.py
+++ b/ipyrad/analysis/pca.py
@@ -199,7 +199,7 @@ def __init__(
             index=self.names, columns=["missing"])
 
         # impute missing data
-        if self._mvals:
+        if (self.impute_method is not False) and self._mvals:
             self._impute_data()
 
 
@@ -231,6 +231,7 @@ def _impute_data(self):
 
         elif self.impute_method == "random":
             missing = self.snps == 9
+            self.snps[missing] = 0
             self.snps[missing] += np.random.choice([0,1,2], self.snps.shape)[missing].astype(np.uint64)
             self._print(
                 "Imputation (Random; sets to ~U[0,1,2]): {:.1f}%, {:.1f}%, {:.1f}%"
@@ -238,7 +239,8 @@ def _impute_data(self):
             )
 
         else:
-            self.snps[self.snps == 9] = 0
+            missing = self.snps == 9
+            self.snps[missing] = 0
             self._print(
                 "Imputation (null; sets to 0): {:.1f}%, {:.1f}%, {:.1f}%"
                 .format(100, 0, 0)