diff --git a/R/import_data.R b/R/import_data.R
index 0b64a7c..f215d86 100644
--- a/R/import_data.R
+++ b/R/import_data.R
@@ -97,12 +97,12 @@ import_data <- function(peak_table, meta_data, format = "none") {
 }
 
 
-unique_compounds <- function(peak_table_list) {
+unique_compounds <- function(peak_table_list, show_message = TRUE) {
   peak_table <- peak_table_list$peak_table
   duplicates <- names(which(table(peak_table$Compound) > 1))
-  if(length(duplicates) > 0){
+  if(length(duplicates) > 0 && show_message){
     cli::cli_inform("Found duplicate compound values, will add a suffix to unique
-                   the value.")
+    the value.")
   }
   for(name in duplicates) {
     idx <- which(peak_table$Compound == name)
@@ -110,6 +110,16 @@ unique_compounds <- function(peak_table_list) {
       peak_table$Compound[[idx[[i]]]] <- paste0(peak_table$Compound[[idx[[i]]]], "_", i)
     }
   }
+
+  # Recursive call to ensure there are no duplicates after fix
+  duplicates <- names(which(table(peak_table$Compound) > 1))
+  
+  if(length(duplicates) > 0){
+    peak_table <- unique_compounds(list(
+      "peak_table" = peak_table,
+      "raw_table" = peak_table
+    ), FALSE)$peak_table
+  }
   return(list(
     "peak_table" = peak_table,
     "raw_table" = peak_table
diff --git a/tests/testthat/test-import_data.R b/tests/testthat/test-import_data.R
index f21c77a..40e9cbe 100644
--- a/tests/testthat/test-import_data.R
+++ b/tests/testthat/test-import_data.R
@@ -47,6 +47,14 @@ test_that("unique_compounds annotate duplicates properly", {
    length(uniqued_list$raw_table$Compound))
 
   expect_false(length(unique(df$Compound)) == length(df$Compound))
+
+  df <- data.frame(Compound = c("1", "1", "1_1", "1_1_1"))
+  ls <- list(peak_table = df, raw_table = df)
+  uniqued_list <- unique_compounds(ls)
+
+  expect_true(uniqued_list$peak_table$Compound[[4]] == "1_1_1_2")
+  expect_true(uniqued_list$peak_table$Compound[[1]] == "1_1_1_1")
+
 })