diff --git a/R/calculatePeptideBindingLoad.R b/R/calculatePeptideBindingLoad.R
index 9730c20..29500b9 100644
--- a/R/calculatePeptideBindingLoad.R
+++ b/R/calculatePeptideBindingLoad.R
@@ -536,6 +536,14 @@ calculatePeptideBindingLoad <- function(
 #'
 #' @keywords internal
 .predictBindingMHCnuggets <- function(peptides, alleles) {
+  # Windows not supported for MHCnuggets
+
+  if (.Platform$OS.type == "windows") {
+    stop("MHCnuggets backend is not supported on Windows due to TensorFlow/HDF5 path limitations. ",
+         "Please use backend='pwm' or backend='netmhcpan' instead.",
+         call. = FALSE)
+  }
+
   results <- data.frame(
     peptide = character(0),
     hla_allele = character(0),
@@ -543,7 +551,6 @@ calculatePeptideBindingLoad <- function(
     stringsAsFactors = FALSE
   )
 
-
   # Run predictions for each allele
   for (allele in alleles) {
     # Determine MHC class from allele name
diff --git a/R/mhcnuggets.R b/R/mhcnuggets.R
index 5d28f4d..2b33724 100644
--- a/R/mhcnuggets.R
+++ b/R/mhcnuggets.R
@@ -41,13 +41,18 @@
 #' }
 #'
 #' @examples
-#' res <- predictMHCnuggets(
-#'   peptides = c("SIINFEKL","LLFGYPVYV"),
-#'   allele   = "A*02:01",
-#'   mhc_class = "I",
-#'   rank_output = TRUE
-#' )
-#' head(res)
+#' \donttest{
+#' # MHCnuggets requires Python/TensorFlow and is not available on Windows
+#' if (.Platform$OS.type != "windows") {
+#'   res <- predictMHCnuggets(
+#'     peptides = c("SIINFEKL","LLFGYPVYV"),
+#'     allele   = "A*02:01",
+#'     mhc_class = "I",
+#'     rank_output = TRUE
+#'   )
+#'   head(res)
+#' }
+#' }
 #'
 #' @section License and Citation:
 #' mhcnuggets is licensed under the GNU General Public License v3.0.
@@ -73,6 +78,13 @@ predictMHCnuggets <- function(peptides,
                               ba_models        = FALSE,
                               rank_output      = FALSE,
                               hla_env          = deepmatchrEnv()) {
+  # ---- Windows not supported ----
+  if (.Platform$OS.type == "windows") {
+    stop("MHCnuggets is not supported on Windows due to TensorFlow/HDF5 path limitations. ",
+         "Please use the 'pwm' or 'netmhcpan' backend, or run on Linux/macOS.",
+         call. = FALSE)
+  }
+
   # ---- fast input checks ----
   if (!is.character(peptides)) stop("`peptides` must be character.")
   if (!length(peptides)) return(data.frame(peptide = character(0L)))
diff --git a/man/predictMHCnuggets.Rd b/man/predictMHCnuggets.Rd
index 262d324..a4e8bf4 100644
--- a/man/predictMHCnuggets.Rd
+++ b/man/predictMHCnuggets.Rd
@@ -87,12 +87,17 @@ GitHub: https://github.com/KarchinLab/mhcnuggets
 }
 
 \examples{
-res <- predictMHCnuggets(
-  peptides = c("SIINFEKL","LLFGYPVYV"),
-  allele   = "A*02:01",
-  mhc_class = "I",
-  rank_output = TRUE
-)
-head(res)
+\donttest{
+# MHCnuggets requires Python/TensorFlow and is not available on Windows
+if (.Platform$OS.type != "windows") {
+  res <- predictMHCnuggets(
+    peptides = c("SIINFEKL","LLFGYPVYV"),
+    allele   = "A*02:01",
+    mhc_class = "I",
+    rank_output = TRUE
+  )
+  head(res)
+}
+}
 
 }
diff --git a/tests/testthat/test-predictMHCnuggets.R b/tests/testthat/test-predictMHCnuggets.R
index 7fe9f1d..d1668b6 100644
--- a/tests/testthat/test-predictMHCnuggets.R
+++ b/tests/testthat/test-predictMHCnuggets.R
@@ -4,6 +4,18 @@ testthat::local_edition(3)
 testthat::skip_if_not_installed("basilisk")
 testthat::skip_if_not_installed("reticulate")
 
+# Test Windows error handling first (before skipping on Windows)
+test_that("predictMHCnuggets errors on Windows", {
+ testthat::skip_if_not(.Platform$OS.type == "windows", "Only runs on Windows")
+ expect_error(
+    predictMHCnuggets(peptides = "SIINFEKL", allele = "A*02:01"),
+    "not supported on Windows"
+  )
+})
+
+# Skip remaining tests on Windows since MHCnuggets is not supported
+testthat::skip_on_os("windows")
+
 # Capture arguments passed through basiliskRun for assertions
 .observed <- new.env(parent = emptyenv())