diff --git a/modules/gltf/gltf_document.cpp b/modules/gltf/gltf_document.cpp
index 95c0ea5f158f..b3e313b9b5a9 100644
--- a/modules/gltf/gltf_document.cpp
+++ b/modules/gltf/gltf_document.cpp
@@ -730,24 +730,40 @@ static Vector<uint8_t> _parse_base64_uri(const String &p_uri) {
 	return buf;
 }
 
+inline bool _all_buffers_empty(const Vector<Vector<uint8_t>> &p_buffers, int start_idx = 0) {
+	for (int i = start_idx; i < p_buffers.size(); i++) {
+		if (!p_buffers[i].is_empty()) {
+			return false;
+		}
+	}
+	return true;
+}
+
 Error GLTFDocument::_encode_buffer_glb(Ref<GLTFState> p_state, const String &p_path) {
 	print_verbose("glTF: Total buffers: " + itos(p_state->buffers.size()));
 
-	if (p_state->buffers.is_empty()) {
+	if (p_state->buffers.is_empty() || _all_buffers_empty(p_state->buffers)) {
+		ERR_FAIL_COND_V_MSG(!p_state->buffer_views.is_empty(), ERR_INVALID_DATA, "glTF: Buffer views are present, but buffers are empty.");
 		return OK;
 	}
 	Array buffers;
-	if (!p_state->buffers.is_empty()) {
-		Vector<uint8_t> buffer_data = p_state->buffers[0];
-		Dictionary gltf_buffer;
+	Dictionary first_buffer;
 
-		gltf_buffer["byteLength"] = buffer_data.size();
-		buffers.push_back(gltf_buffer);
-	}
+	first_buffer["byteLength"] = p_state->buffers[0].size();
+	buffers.push_back(first_buffer);
 
 	for (GLTFBufferIndex i = 1; i < p_state->buffers.size(); i++) {
-		Vector<uint8_t> buffer_data = p_state->buffers[i];
+		const Vector<uint8_t> &buffer_data = p_state->buffers[i];
 		Dictionary gltf_buffer;
+		if (buffer_data.is_empty()) {
+			if (i < p_state->buffers.size() - 1 && !_all_buffers_empty(p_state->buffers, i + 1)) {
+				// Have to push back an empty buffer to avoid changing the buffer index, even though this is against spec.
+				WARN_PRINT("glTF: Buffer " + itos(i) + " is empty, but there are non-empty subsequent buffers.");
+				gltf_buffer["byteLength"] = 0;
+				buffers.push_back(gltf_buffer);
+			}
+			continue;
+		}
 		String filename = p_path.get_basename().get_file() + itos(i) + ".bin";
 		String path = p_path.get_base_dir() + "/" + filename;
 		Error err;
@@ -755,9 +771,6 @@ Error GLTFDocument::_encode_buffer_glb(Ref<GLTFState> p_state, const String &p_p
 		if (file.is_null()) {
 			return err;
 		}
-		if (buffer_data.is_empty()) {
-			return OK;
-		}
 		file->create(FileAccess::ACCESS_RESOURCES);
 		file->store_buffer(buffer_data.ptr(), buffer_data.size());
 		gltf_buffer["uri"] = filename;
@@ -772,14 +785,24 @@ Error GLTFDocument::_encode_buffer_glb(Ref<GLTFState> p_state, const String &p_p
 Error GLTFDocument::_encode_buffer_bins(Ref<GLTFState> p_state, const String &p_path) {
 	print_verbose("glTF: Total buffers: " + itos(p_state->buffers.size()));
 
-	if (p_state->buffers.is_empty()) {
+	if (p_state->buffers.is_empty() || _all_buffers_empty(p_state->buffers)) {
+		ERR_FAIL_COND_V_MSG(!p_state->buffer_views.is_empty(), ERR_INVALID_DATA, "glTF: Buffer views are present, but buffers are empty.");
 		return OK;
 	}
 	Array buffers;
 
 	for (GLTFBufferIndex i = 0; i < p_state->buffers.size(); i++) {
-		Vector<uint8_t> buffer_data = p_state->buffers[i];
+		const Vector<uint8_t> &buffer_data = p_state->buffers[i];
 		Dictionary gltf_buffer;
+		if (buffer_data.is_empty()) {
+			if (i < p_state->buffers.size() - 1 && !_all_buffers_empty(p_state->buffers, i + 1)) {
+				// Have to push back an empty buffer to avoid changing the buffer index, even though this is against spec.
+				WARN_PRINT("glTF: Buffer " + itos(i) + " is empty, but there are non-empty subsequent buffers.");
+				gltf_buffer["byteLength"] = 0;
+				buffers.push_back(gltf_buffer);
+			}
+			continue;
+		}
 		String filename = p_path.get_basename().get_file() + itos(i) + ".bin";
 		String path = p_path.get_base_dir() + "/" + filename;
 		Error err;
@@ -787,16 +810,14 @@ Error GLTFDocument::_encode_buffer_bins(Ref<GLTFState> p_state, const String &p_
 		if (file.is_null()) {
 			return err;
 		}
-		if (buffer_data.is_empty()) {
-			return OK;
-		}
-		file->create(FileAccess::ACCESS_RESOURCES);
 		file->store_buffer(buffer_data.ptr(), buffer_data.size());
 		gltf_buffer["uri"] = filename;
 		gltf_buffer["byteLength"] = buffer_data.size();
 		buffers.push_back(gltf_buffer);
 	}
-	p_state->json["buffers"] = buffers;
+	if (!buffers.is_empty()) {
+		p_state->json["buffers"] = buffers;
+	}
 
 	return OK;
 }