diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index e4f0e9c31..c97e6b32b 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -24,7 +24,9 @@ setGeneric("addProcessHistory", function(object, ...)
 #' present, are subsequently adjusted based on the adjusted retention times
 #' of the MS1 spectra. Note that calling `adjustRtime` on a *xcms* result object
 #' will remove any eventually present previous alignment results as well as
-#' any correspondence analysis results.
+#' any correspondence analysis results. To run a second round of alignment,
+#' raw retention times need to be replaced with adjusted ones using the
+#' [applyAdjustedRtime()] function.
 #'
 #' The alignment method can be specified (and configured) using a dedicated
 #' `param` argument.
diff --git a/R/XcmsExperiment.R b/R/XcmsExperiment.R
index 32e8dd6fd..aef1c0be8 100644
--- a/R/XcmsExperiment.R
+++ b/R/XcmsExperiment.R
@@ -1353,10 +1353,12 @@ setMethod(
     function(object, param, msLevel = 1L, ...) {
         if (!inherits(object, "XcmsExperiment"))
             object <- as(object, "XcmsExperiment")
-        if (hasAdjustedRtime(object)) {
-            message("Removing previous alignment results")
-            object <- dropAdjustedRtime(object)
-        }
+        if (hasAdjustedRtime(object))
+            stop("Alignment results already present. Please either remove ",
+                 "them with 'dropAdjustedRtime' in order to perform an ",
+                 "alternative, new, alignment, or use 'applyAdjustedRtime'",
+                 " prior 'adjustRtime' to perform a second round of ",
+                 "alignment.")
         if (any(msLevel != 1L))
             stop("Alignment is currently only supported for MS level 1")
         if (!nrow(peakGroupsMatrix(param))) {
@@ -1410,8 +1412,11 @@ setMethod("dropAdjustedRtime", "XcmsExperiment", function(object) {
         object@spectra, svs[svs != "rtime_adjusted"])
     object@processHistory <- dropProcessHistoriesList(
         object@processHistory, type = .PROCSTEP.RTIME.CORRECTION, num = 1L)
-    if (hasFeatures(object) && idx_co > idx_al)
+    if (hasFeatures(object) && idx_co > idx_al) {
+        warning("Had to remove feature definitions along with the adjusted ",
+                "retention times because of the dependency between them.")
         object <- dropFeatureDefinitions(object)
+    }
     object
 })
 
diff --git a/man/adjustRtime.Rd b/man/adjustRtime.Rd
index 3ed93450e..70b8182a0 100644
--- a/man/adjustRtime.Rd
+++ b/man/adjustRtime.Rd
@@ -353,7 +353,9 @@ on MS level 1 data. Retention times of spectra from other MS levels, if
 present, are subsequently adjusted based on the adjusted retention times
 of the MS1 spectra. Note that calling \code{adjustRtime} on a \emph{xcms} result object
 will remove any eventually present previous alignment results as well as
-any correspondence analysis results.
+any correspondence analysis results. To run a second round of alignment,
+raw retention times need to be replaced with adjusted ones using the
+\code{\link[=applyAdjustedRtime]{applyAdjustedRtime()}} function.
 
 The alignment method can be specified (and configured) using a dedicated
 \code{param} argument.
diff --git a/tests/testthat/test_XcmsExperiment.R b/tests/testthat/test_XcmsExperiment.R
index 458b754f7..09569ba84 100644
--- a/tests/testthat/test_XcmsExperiment.R
+++ b/tests/testthat/test_XcmsExperiment.R
@@ -464,6 +464,7 @@ test_that("adjustRtime,MsExperiment,PeakGroupsParam works", {
     expect_equal(unname(rtime(xod_xgr)), unname(rtime(res)))
     expect_true(length(res@processHistory) == 3L)
     expect_true(sum(rtime(res) != rtime(a)) > 1000)
+    expect_error(adjustRtime(res, param = pgp), "applyAdjustedRtime")
 
     ## Run with pre-defined anchor peak data
     p <- res@processHistory[[3]]@param