diff --git a/cmd/variables.go b/cmd/variables.go
index 4b259e3f5..e3d7a613c 100644
--- a/cmd/variables.go
+++ b/cmd/variables.go
@@ -63,6 +63,29 @@ func (h *Handler) VariablesSet(ctx context.Context, req *entity.CommandRequest)
 		skipRedeploy = false
 	}
 
+	replace, err := req.Cmd.Flags().GetBool("replace")
+	if err != nil {
+		// The flag is optional; default to false.
+		replace = false
+	}
+
+	yes, err := req.Cmd.Flags().GetBool("yes")
+	if err != nil {
+		// The flag is optional; default to false.
+		yes = false
+	}
+
+	if replace && !yes {
+		fmt.Println(ui.Bold(ui.RedText(fmt.Sprintf("Warning! You are about to fully replace all your variables for the service '%s'.", serviceName)).String()))
+		confirm, err := ui.PromptYesNo("Continue?")
+		if err != nil {
+			return err
+		}
+		if !confirm {
+			return nil
+		}
+	}
+
 	variables := &entity.Envs{}
 	updatedEnvNames := make([]string, 0)
 
@@ -78,7 +101,7 @@ func (h *Handler) VariablesSet(ctx context.Context, req *entity.CommandRequest)
 		updatedEnvNames = append(updatedEnvNames, key)
 	}
 
-	err = h.ctrl.UpsertEnvs(ctx, variables, &serviceName)
+	err = h.ctrl.UpdateEnvs(ctx, variables, &serviceName, replace)
 
 	if err != nil {
 		return err
@@ -89,7 +112,12 @@ func (h *Handler) VariablesSet(ctx context.Context, req *entity.CommandRequest)
 		return err
 	}
 
-	fmt.Print(ui.Heading(fmt.Sprintf("Updated %s for \"%s\"", strings.Join(updatedEnvNames, ", "), environment.Name)))
+	operation := "Updated"
+	if replace {
+		operation = "Replaced existing variables with"
+	}
+
+	fmt.Print(ui.Heading(fmt.Sprintf("%s %s for \"%s\"", operation, strings.Join(updatedEnvNames, ", "), environment.Name)))
 	fmt.Print(ui.KeyValues(*variables))
 
 	if !skipRedeploy {
diff --git a/controller/envs.go b/controller/envs.go
index d33dc28c6..822f97485 100644
--- a/controller/envs.go
+++ b/controller/envs.go
@@ -104,7 +104,7 @@ func (c *Controller) AutoImportDotEnv(ctx context.Context) error {
 			return err
 		}
 		if len(envMap) > 0 {
-			return c.UpsertEnvs(ctx, (*entity.Envs)(&envMap), nil)
+			return c.UpdateEnvs(ctx, (*entity.Envs)(&envMap), nil, false)
 		}
 	}
 	return nil
@@ -134,7 +134,7 @@ func (c *Controller) SaveEnvsToFile(ctx context.Context) error {
 	return nil
 }
 
-func (c *Controller) UpsertEnvs(ctx context.Context, envs *entity.Envs, serviceName *string) error {
+func (c *Controller) UpdateEnvs(ctx context.Context, envs *entity.Envs, serviceName *string, replace bool) error {
 	projectCfg, err := c.GetProjectConfigs(ctx)
 	if err != nil {
 		return err
@@ -185,12 +185,13 @@ func (c *Controller) UpsertEnvs(ctx context.Context, envs *entity.Envs, serviceN
 		}
 	}
 
-	return c.gtwy.UpsertVariablesFromObject(ctx, &entity.UpdateEnvsRequest{
+	return c.gtwy.UpdateVariablesFromObject(ctx, &entity.UpdateEnvsRequest{
 		ProjectID:     projectCfg.Project,
 		EnvironmentID: projectCfg.Environment,
 		PluginID:      pluginID,
 		ServiceID:     serviceID,
 		Envs:          envs,
+		Replace:       replace,
 	})
 }
 
diff --git a/entity/envs.go b/entity/envs.go
index 0a490dd76..d285ef37c 100644
--- a/entity/envs.go
+++ b/entity/envs.go
@@ -18,6 +18,7 @@ type UpdateEnvsRequest struct {
 	PluginID      string
 	ServiceID     string
 	Envs          *Envs
+	Replace       bool
 }
 
 type DeleteVariableRequest struct {
diff --git a/gateway/envs.go b/gateway/envs.go
index a82555661..3c3af2cc2 100644
--- a/gateway/envs.go
+++ b/gateway/envs.go
@@ -2,6 +2,7 @@ package gateway
 
 import (
 	"context"
+	"fmt"
 
 	"github.com/railwayapp/cli/entity"
 )
@@ -32,12 +33,19 @@ func (g *Gateway) GetEnvs(ctx context.Context, req *entity.GetEnvsRequest) (*ent
 	return resp.Envs, nil
 }
 
-func (g *Gateway) UpsertVariablesFromObject(ctx context.Context, req *entity.UpdateEnvsRequest) error {
-	gqlReq, err := g.NewRequestWithAuth(`
+func (g *Gateway) UpdateVariablesFromObject(ctx context.Context, req *entity.UpdateEnvsRequest) error {
+	queryName := "upsertVariablesFromObject"
+
+	if req.Replace {
+		// When replacing, use the set query which will blow away all old variables and only set the ones in this query
+		queryName = "variablesSetFromObject"
+	}
+
+	gqlReq, err := g.NewRequestWithAuth(fmt.Sprintf(`
 	  	mutation($projectId: String!, $environmentId: String!, $pluginId: String, $serviceId: String, $variables: Json!) {
-				upsertVariablesFromObject(projectId: $projectId, environmentId: $environmentId, pluginId: $pluginId, serviceId: $serviceId, variables: $variables)
+				%s(projectId: $projectId, environmentId: $environmentId, pluginId: $pluginId, serviceId: $serviceId, variables: $variables)
 	  	}
-	`)
+	`, queryName))
 	if err != nil {
 		return err
 	}
diff --git a/main.go b/main.go
index d3dfbcfa8..ba0bd724b 100644
--- a/main.go
+++ b/main.go
@@ -154,6 +154,8 @@ func init() {
 	variablesCmd.AddCommand(variablesSetCmd)
 	variablesSetCmd.Flags().StringP("service", "s", "", "Fetch variables accessible to a specific service")
 	variablesSetCmd.Flags().Bool("skip-redeploy", false, "Skip redeploying the specified service after changing the variables")
+	variablesSetCmd.Flags().Bool("replace", false, "Fully replace all previous variables instead of updating them")
+	variablesSetCmd.Flags().Bool("yes", false, "Skip all confirmation dialogs")
 
 	variablesDeleteCmd := &cobra.Command{
 		Use:     "delete key",