diff --git a/R/read.magpie.R b/R/read.magpie.R
index 9935d46e..7d1882c1 100644
--- a/R/read.magpie.R
+++ b/R/read.magpie.R
@@ -131,6 +131,7 @@ read.magpie <- function(file_name, file_folder = "", file_type = NULL, # nolint:
       }
 
       readMagpie <- clean_magpie(as.magpie(x))
+      attr(readMagpie, "crs") <- NULL
     } else {
       if (!requireNamespace("raster", quietly = TRUE)) {
         stop("The package \"raster\" is required!")
diff --git a/R/write.magpie.R b/R/write.magpie.R
index 0c36f824..a80626ef 100644
--- a/R/write.magpie.R
+++ b/R/write.magpie.R
@@ -211,6 +211,9 @@ write.magpie <- function(x, # nolint: object_name_linter, cyclocomp_linter.
       if (!requireNamespace("ncdf4", quietly = TRUE) || !requireNamespace("terra", quietly = TRUE)) {
         stop("The packages \"ncdf4\" and \"terra\" are required!")
       }
+      if (is.null(getItems(x, 3))) {
+        getItems(x, 3) <- "Variable"
+      }
       spatRasterDataset <- as.SpatRasterDataset(x)
 
       if (zname != "time") {
diff --git a/tests/testthat/test-readwritemagpie.R b/tests/testthat/test-readwritemagpie.R
index 616bdb6d..0434b904 100644
--- a/tests/testthat/test-readwritemagpie.R
+++ b/tests/testthat/test-readwritemagpie.R
@@ -87,29 +87,28 @@ test_that("handling of spatial data works", {
   expect_no_warning(write.magpie(m10, file.path(td, "test.nc")))
   expect_silent(write.magpie(m05, file.path(td, "test.nc")))
   expect_silent(m05in <- read.magpie(file.path(td, "test.nc")))
+
   getCoords(m05) <- magclass:::magclassdata$half_deg[c("lon", "lat")]
   m05 <- collapseDim(m05, dim = c(1.1, 1.2))
   m05 <- m05[getItems(m05in, dim = 1), , ]
   getNames(m05in) <- NULL
   getSets(m05in, fulldim = FALSE)[3] <- "data"
-  attr(m05in, ".internal.selfref")  <- NULL # nolint
   expect_identical(m05, m05in)
 
   a <- maxample("animal")
   a <- dimSums(a, dim = c(1.3, 1.4, 2, 3))
   write.magpie(a, file.path(td, "animal.asc"))
-  copy.magpie(file.path(td, "animal.asc"), file.path(td, "animal.nc"))
   asc <- read.magpie(file.path(td, "animal.asc"))
-  expect_silent(anc <- read.magpie(file.path(td, "animal.nc")))
+  attr(asc, ".internal.selfref")  <- NULL # nolint
+  getItems(asc, dim = 2) <- NULL
+  getItems(asc, dim = 3) <- NULL
+  expect_identical(asc, a)
 
-  .clean <- function(x) {
-    attr(x, ".internal.selfref")  <- NULL # nolint
-    getItems(x, dim = 2) <- NULL
-    getItems(x, dim = 3) <- NULL
-    return(x)
-  }
-  expect_identical(.clean(asc), a)
-  expect_identical(.clean(anc), a)
+  write.magpie(a, file.path(td, "animal.nc"))
+  expect_silent(anc <- read.magpie(file.path(td, "animal.nc")))
+  getItems(anc, dim = 3) <- NULL
+  getSets(anc) <- c("x", "y", "d2", "d3")
+  expect_identical(anc, a)
 })