diff --git a/internal/agent/upgrade.go b/internal/agent/upgrade.go
index e6980707..6b679241 100644
--- a/internal/agent/upgrade.go
+++ b/internal/agent/upgrade.go
@@ -3,6 +3,7 @@ package agent
 import (
 	"encoding/json"
 	"fmt"
+	"path/filepath"
 	"strings"
 
 	hook "github.com/kairos-io/kairos-agent/v2/internal/agent/hooks"
@@ -13,6 +14,7 @@ import (
 	config "github.com/kairos-io/kairos-agent/v2/pkg/config"
 	"github.com/kairos-io/kairos-agent/v2/pkg/uki"
 	internalutils "github.com/kairos-io/kairos-agent/v2/pkg/utils"
+	k8sutils "github.com/kairos-io/kairos-agent/v2/pkg/utils/k8s"
 	events "github.com/kairos-io/kairos-sdk/bus"
 	"github.com/kairos-io/kairos-sdk/collector"
 	"github.com/kairos-io/kairos-sdk/utils"
@@ -68,10 +70,19 @@ func Upgrade(
 	source string, force, strictValidations bool, dirs []string, upgradeEntry string, preReleases bool) error {
 	bus.Manager.Initialize()
 
+	fixedDirs := make([]string, len(dirs))
+	// Check and fix dirs if we are under k8s, so we read the actual running system configs instead of only
+	// the container configs
+	// we can run it blindly as it will return an empty string if not under k8s
+	hostdir := k8sutils.GetHostDirForK8s()
+	for _, dir := range dirs {
+		fixedDirs = append(fixedDirs, filepath.Join(hostdir, dir))
+	}
+
 	if internalutils.UkiBootMode() == internalutils.UkiHDD {
-		return upgradeUki(source, dirs, upgradeEntry, strictValidations)
+		return upgradeUki(source, fixedDirs, upgradeEntry, strictValidations)
 	} else {
-		return upgrade(source, dirs, upgradeEntry, strictValidations)
+		return upgrade(source, fixedDirs, upgradeEntry, strictValidations)
 	}
 }
 
diff --git a/pkg/config/spec.go b/pkg/config/spec.go
index 7e023ed7..842b6244 100644
--- a/pkg/config/spec.go
+++ b/pkg/config/spec.go
@@ -27,6 +27,7 @@ import (
 	"github.com/kairos-io/kairos-agent/v2/pkg/constants"
 	v1 "github.com/kairos-io/kairos-agent/v2/pkg/types/v1"
 	fsutils "github.com/kairos-io/kairos-agent/v2/pkg/utils/fs"
+	k8sutils "github.com/kairos-io/kairos-agent/v2/pkg/utils/k8s"
 	"github.com/kairos-io/kairos-agent/v2/pkg/utils/partitions"
 	"github.com/kairos-io/kairos-sdk/collector"
 	"github.com/kairos-io/kairos-sdk/ghw"
@@ -849,17 +850,11 @@ func GetSourceSize(config *Config, source *v1.ImageSource) (int64, error) {
 		// , which mounts the host root into $HOST_DIR
 		// we should skip that dir when calculating the size as we would be doubling the calculated size
 		// Plus we will hit the usual things when checking a running system. Processes that go away, tmpfiles, etc...
-
 		// This is always set for pods running under kubernetes
 		_, underKubernetes := os.LookupEnv("KUBERNETES_SERVICE_HOST")
-		config.Logger.Logger.Info().Bool("status", underKubernetes).Msg("Running under kubernetes")
 		// Try to get the HOST_DIR in case we are not using the default one
-		hostDir := os.Getenv("HOST_DIR")
-		// If we are under kubernetes but the HOST_DIR var is empty, default to /host as system-upgrade-controller mounts
-		// the host in that dir by default
-		if underKubernetes && hostDir == "" {
-			hostDir = "/host"
-		}
+		hostDir := k8sutils.GetHostDirForK8s()
+		config.Logger.Logger.Debug().Bool("status", underKubernetes).Str("hostdir", hostDir).Msg("Kubernetes check")
 		err = fsutils.WalkDirFs(config.Fs, source.Value(), func(path string, d fs.DirEntry, err error) error {
 			// If its empty we are just not setting it, so probably out of the k8s upgrade path
 			if hostDir != "" && strings.HasPrefix(path, hostDir) {
diff --git a/pkg/config/spec_test.go b/pkg/config/spec_test.go
index 2ba568ba..93072b7b 100644
--- a/pkg/config/spec_test.go
+++ b/pkg/config/spec_test.go
@@ -703,7 +703,8 @@ var _ = Describe("GetSourceSize", Label("GetSourceSize"), func() {
 
 		Expect(os.Mkdir(filepath.Join(tempDir, "host"), os.ModePerm)).ToNot(HaveOccurred())
 		Expect(createFileOfSizeInMB(filepath.Join(tempDir, "host", "what.txt"), 200)).ToNot(HaveOccurred())
-		// Set env var like the suc upgrade does
+		// Set env var like the suc upgrade and k8s does to trigger the skip
+		Expect(os.Setenv("KUBERNETES_SERVICE_HOST", "10.0.0.1")).ToNot(HaveOccurred())
 		Expect(os.Setenv("HOST_DIR", filepath.Join(tempDir, "host"))).ToNot(HaveOccurred())
 
 		sizeAfter, err := config.GetSourceSize(conf, imageSource)
diff --git a/pkg/utils/k8s/common.go b/pkg/utils/k8s/common.go
new file mode 100644
index 00000000..267c0972
--- /dev/null
+++ b/pkg/utils/k8s/common.go
@@ -0,0 +1,27 @@
+package k8s
+
+import "os"
+
+// GetHostDirForK8s returns the base dir where the system is
+// This is because under k8s, we mount the actual system under a dir
+// So we need to know which paths we need to read the configs from
+// if we read them from the root directly, we are actually reading the
+// configs of the upgrade container
+// If not found returns an empty string
+func GetHostDirForK8s() string {
+	_, underKubernetes := os.LookupEnv("KUBERNETES_SERVICE_HOST")
+	// Try to get the HOST_DIR in case we are not using the default one
+	hostDirEnv := os.Getenv("HOST_DIR")
+	// If we are under kubernetes but the HOST_DIR var is empty, default to /host as system-upgrade-controller mounts
+	// the host in that dir by default
+	if underKubernetes {
+		if hostDirEnv != "" {
+			return hostDirEnv
+		} else {
+			return "/host"
+		}
+	} else {
+		// We return an empty string so any filepath.join does not alter the paths
+		return ""
+	}
+}