diff --git a/R/plotly_build.R b/R/plotly_build.R
index 2cf5de65aa..abaa8e5b61 100644
--- a/R/plotly_build.R
+++ b/R/plotly_build.R
@@ -280,10 +280,12 @@ plotly_build.plotly <- function(p, registerFrames = TRUE) {
     )
     for (i in x$.plotlyVariableMapping) {
       # try to reduce the amount of data we have to send for non-positional scales
-      x[[i]] <- structure(
-        if (i %in% npscales()) uniq(d[[i]]) else d[[i]],
-        class = oldClass(x[[i]])
-      )
+      entry <- if (i %in% npscales()) uniq(d[[i]]) else d[[i]]
+      if (is.null(entry)) {
+        x[[i]] <- NULL  
+      } else {
+        x[[i]] <- structure(entry, class = oldClass(x[[i]]))  
+      }
     }
     x
   })
diff --git a/tests/testthat/test-ggplot-lines.R b/tests/testthat/test-ggplot-lines.R
index 08095c8694..e0d437985a 100644
--- a/tests/testthat/test-ggplot-lines.R
+++ b/tests/testthat/test-ggplot-lines.R
@@ -120,3 +120,10 @@ test_that("geom_linerange() without a y aesthetic translates to a path", {
   )
   
 })
+
+test_that("NA values do not cause a lot of warnings when ploting (#1299)", {
+  df <- data.frame(x=1:2, y=NA)
+  p <- plot_ly(df, x=~x, y=~y)
+  expect_warning(plotly_build(p), "Ignoring")
+  expect_failure(expect_warning(plotly_build(p), "structure"))
+})