diff --git a/R/merge_sce_list.R b/R/merge_sce_list.R
index f6bb60c4..463dc10a 100644
--- a/R/merge_sce_list.R
+++ b/R/merge_sce_list.R
@@ -83,6 +83,9 @@ merge_sce_list <- function(
      Please check that `retain_coldata_cols` was correctly specified.")
   }
 
+  # Check metadata - library_id and sample_id must be present
+  check_metadata(sce_list)
+
   # Check altExp compatibility, if we are including them
   # altExps for a given name must all have the same features and the same assays
   if (include_altexp) {
@@ -102,6 +105,17 @@ merge_sce_list <- function(
 
     # Update retain_coldata_cols
     retain_coldata_cols <- c(retain_coldata_cols, altexp_columns)
+
+    # Check each altExp metadata, for SCEs with the altExp
+    names(altexp_attributes) |>
+      purrr::walk(
+        \(altexp_name) {
+          sce_list |>
+            purrr::keep(\(sce) altexp_name %in% altExpNames(sce)) |>
+            purrr::map(altExp, altexp_name) |>
+            check_metadata()
+        }
+      )
   } else {
     # Remove altexps if we are not including them
     sce_list <- sce_list |>
@@ -136,17 +150,6 @@ merge_sce_list <- function(
     warning("The provided `retain_coldata_cols` are not present in any SCEs.")
   }
 
-  # check that library id and sample id are present in metadata
-  id_checks <- sce_list |>
-    purrr::map(\(sce) {
-      all(c("library_id", "sample_id") %in% names(metadata(sce)))
-    }) |>
-    unlist()
-
-  if (!all(id_checks)) {
-    stop("The metadata for each SCE object must contain `library_id` and `sample_id`.")
-  }
-
   ## Prepare main experiment of SCEs for merging --------------------
   sce_list <- sce_list |>
     purrr::imap(
@@ -159,45 +162,7 @@ merge_sce_list <- function(
     )
 
 
-  ## Handle metadata ---------------------------------------------
-  # get a list of metadata from the list of sce objects
-  # each library becomes an element within the metadata components
-  metadata_list <- sce_list |>
-    purrr::map(metadata) |>
-    purrr::transpose()
-
-  # flatten and reduce the library ids and sample ids
-  metadata_list$library_id <- metadata_list$library_id |>
-    unlist() |>
-    unique()
-
-  metadata_list$sample_id <- metadata_list$sample_id |>
-    unlist() |>
-    unique()
-
-  # if object has sample metadata then combine into a single data frame
-  if ("sample_metadata" %in% names(metadata_list)) {
-    sample_metadata <- metadata_list$sample_metadata |>
-      purrr::map(\(df) {
-        # make sure all column types are compatible first
-        df |>
-          dplyr::mutate(dplyr::across(dplyr::everything(), as.character))
-      }) |>
-      dplyr::bind_rows() |>
-      unique()
-
-    # check that all sample ids are found in the new sample metadata and warn if not
-    if (!all(metadata_list$sample_id %in% sample_metadata$sample_id)) {
-      warning("Not all sample ids are present in metadata(merged_sce)$sample_metadata.")
-    }
-
-    # replace sample metadata in metadata list
-    metadata_list$sample_metadata <- sample_metadata
-  }
-
-
   ## Handle altExps ------------------------------------------------------
-
   # If we are including altExps, process them and save to list to add to merged SCE
   if (include_altexp) {
     for (altexp_name in names(altexp_attributes)) {
@@ -219,8 +184,35 @@ merge_sce_list <- function(
   # Create the merged SCE from the processed list
   merged_sce <- do.call(combineCols, unname(sce_list))
 
-  # Replace existing metadata list with merged metadata
-  metadata(merged_sce) <- metadata_list
+  # Update metadata in merged objects, using the unmerged sce_list
+  metadata(merged_sce) <- sce_list |>
+    purrr::map(metadata) |>
+    prepare_merged_metadata()
+
+  if (include_altexp) {
+    for (altexp_name in names(altexp_attributes)) {
+      has_altexp_name <- sce_list |>
+        purrr::map_lgl(\(sce) (altexp_name %in% altExpNames(sce)))
+
+      # For any SCEs without this altExp, create the library_id and sample_id metadata
+      additional_metadata <- sce_list |>
+        purrr::discard(has_altexp_name) |>
+        purrr::map(extract_metadata_for_altexp)
+
+      # Update metadata in altExps that were originally present
+      altexp_metadata_list <- sce_list |>
+        purrr::keep(has_altexp_name) |>
+        purrr::map(altExp, altexp_name) |>
+        purrr::map(metadata) |>
+        # Tack on the metadata we created for libraries without altExps
+        c(additional_metadata)
+
+      # Ensure correct order
+      altexp_metadata_list <- altexp_metadata_list[names(sce_list)]
+
+      metadata(altExp(merged_sce, altexp_name)) <- prepare_merged_metadata(altexp_metadata_list)
+    }
+  }
 
   return(merged_sce)
 }
@@ -304,9 +296,6 @@ prepare_sce_for_merge <- function(
     colnames(sce) <- glue::glue("{sce_name}-{colnames(sce)}")
   }
 
-  # Update metadata list
-  metadata(sce) <- update_sce_metadata(metadata(sce))
-
   # return the processed SCE
   return(sce)
 }
@@ -358,39 +347,6 @@ prepare_altexp_for_merge <- function(
 }
 
 
-
-#' Helper function to update SCE metadata for merging
-#'
-#' @param metadata_list Current SCE metadata before modification
-#'
-#' @return Updated metadata list to store in the SCE
-update_sce_metadata <- function(metadata_list) {
-  # first check that this library hasn't already been merged
-  if ("library_metadata" %in% names(metadata_list)) {
-    stop(paste(
-      "This SCE object appears to be a merged object",
-      "We do not support merging objects with objects that have already been merged."
-    ))
-  }
-
-  # create library and sample metadata.
-  # library metadata will hold all the previous metadata fields, to avoid conflicts
-  library_metadata <- metadata_list[names(metadata_list) != "sample_metadata"]
-  sample_metadata <- metadata_list$sample_metadata
-
-  # combine into one list
-  metadata_list <- list(
-    library_id = metadata_list[["library_id"]],
-    sample_id = metadata_list[["sample_id"]],
-    library_metadata = library_metadata, # this will be all previous metadata for the given library
-    sample_metadata = sample_metadata # this will be the same as the previous sample_metadata
-  )
-
-  # return updated metadata
-  return(metadata_list)
-}
-
-
 #' Helper function to check altExp compatibility
 #'
 #' @param sce_list List of SCEs with altExps to check
@@ -445,3 +401,118 @@ get_altexp_attributes <- function(sce_list) {
   }
   return(altexp_attributes)
 }
+
+
+
+
+
+#' Prepare an updated list of metadata for the merged SCE
+#'
+#' The metadata will be reformatted to contain the following fields:
+#' - `library_id`:       vector of all library ids in the merged object
+#' - `sample_id`:        vector of all sample ids in the merged object
+#' - `library_metadata`: pre-merge metadata list for each library, named by SCE name
+#' - `sample_metadata`:  a data frame with all distinct rows from the pre-merge sample_metadata data frames,
+#'   with all values coerced to character
+#'
+#' @param metadata_list List of metadata to update
+#'
+#' @return Updated metadata list to include in the merged SCE
+prepare_merged_metadata <- function(metadata_list) {
+  # Define vectors of library and sample ids
+  metadata_library_ids <- metadata_list |>
+    purrr::map_chr("library_id")
+
+  metadata_sample_ids <- metadata_list |>
+    purrr::map_chr("sample_id")
+
+  # Grab names to check contents
+  transposed_names <- metadata_list |>
+    purrr::map(names) |>
+    purrr::reduce(union)
+
+  # first check that this library hasn't already been merged
+  if ("library_metadata" %in% transposed_names) {
+    stop(paste(
+      "This SCE object appears to be a merged object",
+      "We do not support merging objects with objects that have already been merged."
+    ))
+  }
+
+  # Create new version of metadata_list without any sample_metadata fields
+  # Note that this will work even if `sample_metadata` is not present
+  library_metadata <- metadata_list |>
+    purrr::map(
+      \(meta) meta[which(names(meta) != "sample_metadata")]
+    )
+
+  # combine into final metadata list
+  final_metadata_list <- list(
+    # vector of all library ids
+    library_id = metadata_library_ids,
+    # vector of all sample ids
+    sample_id = metadata_sample_ids,
+    # list of existing metadata for each library, with sample_metadata removed
+    library_metadata = library_metadata
+  )
+
+  # if object has sample metadata then combine into a single data frame,
+  #  and add this to the final_metadata_list
+  if ("sample_metadata" %in% transposed_names) {
+    sample_metadata <- metadata_list |>
+      purrr::map("sample_metadata") |>
+      purrr::map(\(df) {
+        # make sure all column types are compatible first
+        df |>
+          dplyr::mutate(dplyr::across(dplyr::everything(), as.character))
+      }) |>
+      dplyr::bind_rows() |>
+      dplyr::distinct()
+
+    # check that all sample ids are found in the new sample metadata and warn if not
+    if (!all(metadata_sample_ids %in% sample_metadata$sample_id)) {
+      warning("Not all sample ids are present in metadata(merged_sce)$sample_metadata.")
+    }
+
+    # add to final_metadata_list
+    final_metadata_list$sample_metadata <- sample_metadata
+  }
+
+  return(final_metadata_list)
+}
+
+
+
+#' Helper function to check that expected metadata fields are present in a given
+#' list of SCEs.
+#'
+#' The default expected fields are `library_id` and `sample_id`. If either is missing from
+#'   any SCE, an error is thrown. This function does not return anything.
+#'
+#' @param sce_list List of SCEs to check
+#' @param expected_fields a vector of metadata fields that should be present
+check_metadata <- function(sce_list, expected_fields = c("library_id", "sample_id")) {
+  metadata_checks <- sce_list |>
+    purrr::map_lgl(\(sce) {
+      all(expected_fields %in% names(metadata(sce)))
+    })
+
+  if (!all(metadata_checks)) {
+    stop(glue::glue("
+       The metadata for each SCE object must contain {stringr::str_flatten_comma(expected_fields, ', and ')}.
+       If `include_altexp` is TRUE, these fields must also be present in all altExps.
+     "))
+  }
+}
+
+#' Helper function to extract main SCE metadata for inclusion in an altExp
+#'
+#' @param sce SCE object to extract metadata from
+#'
+#' @return List with fields `library_id` and `sample_id`
+extract_metadata_for_altexp <- function(sce) {
+  list(
+    library_id = metadata(sce)$library_id,
+    sample_id = metadata(sce)$sample_id
+  )
+}
diff --git a/inst/WORDLIST b/inst/WORDLIST
index eb418099..3439328a 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -1,3 +1,5 @@
+
+altExp
 Alevin
 CMD
 commenter
@@ -5,6 +7,8 @@ Dockerfile
 Kallisto
 nf
 pre
+SCE
+SCEs
 PRs
 RStudio
 ScPCA
diff --git a/man/check_metadata.Rd b/man/check_metadata.Rd
new file mode 100644
index 00000000..0b9fa0a8
--- /dev/null
+++ b/man/check_metadata.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/merge_sce_list.R
+\name{check_metadata}
+\alias{check_metadata}
+\title{Helper function to check that expected metadata fields are present in a given
+list of SCEs.}
+\usage{
+check_metadata(sce_list, expected_fields = c("library_id", "sample_id"))
+}
+\arguments{
+\item{sce_list}{List of SCEs to check}
+
+\item{expected_fields}{a vector of metadata fields that should be present}
+}
+\description{
+The fields `library_id` and `sample_id` must be present. If either is missing from
+  any SCE, an error is thrown. This function does not return anything.
+}
diff --git a/man/extract_metadata_for_altexp.Rd b/man/extract_metadata_for_altexp.Rd
new file mode 100644
index 00000000..f7243854
--- /dev/null
+++ b/man/extract_metadata_for_altexp.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/merge_sce_list.R
+\name{extract_metadata_for_altexp}
+\alias{extract_metadata_for_altexp}
+\title{Helper function to extract main SCE metadata for inclusion in an altExp}
+\usage{
+extract_metadata_for_altexp(sce)
+}
+\arguments{
+\item{sce}{SCE object to extract metadata from}
+}
+\value{
+List with fields `library_id` and `sample_id`
+}
+\description{
+Helper function to extract main SCE metadata for inclusion in an altExp
+}
diff --git a/man/prepare_merged_metadata.Rd b/man/prepare_merged_metadata.Rd
new file mode 100644
index 00000000..3e1905c6
--- /dev/null
+++ b/man/prepare_merged_metadata.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/merge_sce_list.R
+\name{prepare_merged_metadata}
+\alias{prepare_merged_metadata}
+\title{Prepare an updated list of metadata for the merged SCE}
+\usage{
+prepare_merged_metadata(metadata_list)
+}
+\arguments{
+\item{metadata_list}{List of metadata to update}
+}
+\value{
+Updated metadata list to include in the merged SCE
+}
+\description{
+The metadata will be reformatted to contain the following fields:
+- `library_id`:       vector of all library ids in the merged object
+- `sample_id`:        vector of all sample ids in the merged object
+- `library_metadata`: pre-merge metadata list for each library, named by SCE name
+- `sample_metadata`:  a data frame with all distinct rows from the pre-merge sample_metadata data frames,
+  with all values coerced to character
+}
diff --git a/man/update_sce_metadata.Rd b/man/update_sce_metadata.Rd
deleted file mode 100644
index 1cc58743..00000000
--- a/man/update_sce_metadata.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/merge_sce_list.R
-\name{update_sce_metadata}
-\alias{update_sce_metadata}
-\title{Helper function to update SCE metadata for merging}
-\usage{
-update_sce_metadata(metadata_list)
-}
-\arguments{
-\item{metadata_list}{Current SCE metadata before modification}
-}
-\value{
-Updated metadata list to store in the SCE
-}
-\description{
-Helper function to update SCE metadata for merging
-}
diff --git a/tests/testthat/test-merge_sce_list.R b/tests/testthat/test-merge_sce_list.R
index 991909e6..fa5c5ea6 100644
--- a/tests/testthat/test-merge_sce_list.R
+++ b/tests/testthat/test-merge_sce_list.R
@@ -59,23 +59,6 @@ sce_list <- list(
 
 # Tests without altexps ----------------------------------------------
 
-test_that("`update_sce_metadata()` returns the expected list", {
-  metadata_list <- metadata(sce_list[[1]])
-
-  new_metadata <- update_sce_metadata(metadata_list)
-
-  expect_equal(
-    names(new_metadata),
-    c("library_id", "sample_id", "library_metadata", "sample_metadata")
-  )
-
-  expect_equal(
-    names(new_metadata$library_metadata),
-    c("library_id", "sample_id", "total_reads")
-  )
-})
-
-
 test_that("`prepare_sce_for_merge` works as expected when all columns are present, no altexps", {
   result_sce <- prepare_sce_for_merge(
     sce,
@@ -114,26 +97,6 @@ test_that("`prepare_sce_for_merge` works as expected when all columns are presen
     names(rowData(result_sce)),
     c("gene_names", paste(sce_name, "other_column", sep = "-"))
   )
-
-  # metadata names check
-  expect_contains(
-    names(metadata(result_sce)),
-    c("library_id", "sample_id", "library_metadata", "sample_metadata")
-  )
-
-  # check that sample metadata is a data frame
-  expect_s3_class(metadata(result_sce)$sample_metadata, "data.frame")
-
-  # check that contents of library id and sample id are correct
-  expect_equal(
-    metadata(result_sce)$library_id,
-    "library-1"
-  )
-
-  expect_equal(
-    metadata(result_sce)$sample_id,
-    "sample-1"
-  )
 })
 
 
@@ -511,7 +474,18 @@ test_that("merging SCEs with 1 altexp but different features fails as expected,
 
 
 test_that("merging SCEs where 1 altExp is missing works as expected, with altexps", {
-  sce_list_with_altexp[["sce4"]] <- sce_list[[1]]
+  sce_list_with_altexp$sce4 <- sce_list[[1]]
+
+  # update the metdata list with sce4 name
+  metadata(sce_list_with_altexp$sce4) <- list(
+    library_id = "library-sce4",
+    sample_id = "sample-sce4",
+    total_reads = 100,
+    sample_metadata = data.frame(
+      sample_id = "sample-sce4",
+      library_id = "library-sce4"
+    )
+  )
 
   merged_sce <- merge_sce_list(
     sce_list_with_altexp,
@@ -526,6 +500,57 @@ test_that("merging SCEs where 1 altExp is missing works as expected, with altexp
 
   merged_altexp <- altExp(merged_sce, "adt")
 
+  # check merged_altexp metadata
+  altexp_metadata <- metadata(merged_altexp)
+  expect_setequal(
+    names(altexp_metadata),
+    c("library_id", "sample_id", "library_metadata")
+  )
+  expect_setequal(
+    altexp_metadata$library_id,
+    glue::glue("library-{names(sce_list_with_altexp)}")
+  )
+  expect_setequal(
+    altexp_metadata$sample_id,
+    glue::glue("sample-{names(sce_list_with_altexp)}")
+  )
+
+
+  expect_setequal(
+    # all but sce4 contain all metadata components
+    altexp_metadata$library_metadata[-4] |>
+      purrr::map(names) |>
+      purrr::reduce(intersect),
+    c("library_id", "sample_id", "mapped_reads", "ambient_profile")
+  )
+
+  expect_setequal(
+    # sce4 has only library id and sample id, as it was missing the altExp
+    names(altexp_metadata$library_metadata$sce4),
+    c("library_id", "sample_id")
+  )
+
+
+  expect_true(
+    is.null(altexp_metadata$library_metadata$sce4$ambient_profile) &
+      is.null(altexp_metadata$library_metadata$sce4$mapped_reads)
+  )
+  expect_true(
+    all(
+      is.numeric(altexp_metadata$library_metadata$sce1$ambient_profile),
+      is.numeric(altexp_metadata$library_metadata$sce2$ambient_profile),
+      is.numeric(altexp_metadata$library_metadata$sce3$ambient_profile)
+    )
+  )
+  expect_true(
+    all(
+      altexp_metadata$library_metadata$sce1$library_id == "library-sce1",
+      altexp_metadata$library_metadata$sce2$library_id == "library-sce2",
+      altexp_metadata$library_metadata$sce3$library_id == "library-sce3",
+      altexp_metadata$library_metadata$sce4$library_id == "library-sce4"
+    )
+  )
+
   # check dimensions
   expect_equal(
     dim(merged_sce),
@@ -533,8 +558,9 @@ test_that("merging SCEs where 1 altExp is missing works as expected, with altexp
   )
   expect_equal(
     dim(merged_altexp),
-    c(num_altexp_features, total_cells * 4 / 3 )
+    c(num_altexp_features, total_cells * 4 / 3)
   )
+
   # check colData names are as expected
   expected_coldata <- c(
     "sum",
@@ -580,3 +606,86 @@ test_that("get_altexp_attributes throws an error as expected when features do no
   altExp(sce_list_with_altexp[[1]]) <- altExp(sce_list_with_altexp[[1]])[1:3, ]
   expect_error(get_altexp_attributes(sce_list_with_altexp))
 })
+
+
+test_that("check_metadata throws an error when a field is missing", {
+  metadata(sce_list[[1]])$library_id <- NULL
+  expect_error(check_metadata(sce_list))
+  expect_no_error(check_metadata(sce_list, expected_fields = "sample_id"))
+})
+
+test_that("extract_metadata_for_altexp returns the correct values", {
+  expected_list <- list(
+    "library_id" = "library-sce1",
+    "sample_id"  = "sample-sce1"
+  )
+  observed_list <- extract_metadata_for_altexp(sce_list[[1]])
+  expect_equal(observed_list, expected_list)
+})
+
+test_that("prepare_merged_metadata works as expected, with sample_metadata present", {
+  observed_metadata <- sce_list |>
+    purrr::map(metadata) |>
+    prepare_merged_metadata()
+
+  expect_setequal(
+    names(observed_metadata),
+    c("library_id", "sample_id", "library_metadata", "sample_metadata")
+  )
+
+  expected_library_ids <- glue::glue("library-{names(sce_list)}")
+  expected_sample_ids <- glue::glue("sample-{names(sce_list)}")
+  expect_setequal(
+    observed_metadata$library_id,
+    expected_library_ids
+  )
+  expect_setequal(
+    observed_metadata$sample_id,
+    expected_sample_ids
+  )
+  expect_setequal(
+    names(observed_metadata$library_metadata),
+    names(sce_list)
+  )
+  expect_setequal(
+    observed_metadata$library_metadata |>
+      purrr::map(names) |>
+      purrr::reduce(intersect),
+    c("library_id", "sample_id", "total_reads")
+  )
+  expect_equal(
+    data.frame(
+      sample_id = expected_sample_ids,
+      library_id = expected_library_ids
+    ),
+    observed_metadata$sample_metadata
+  )
+})
+
+
+test_that("prepare_merged_metadata works as expected from altExps metadata (aka, sample_metadata NOT present)", {
+  observed_metadata <- sce_list_with_altexp |>
+    purrr::map(altExp) |>
+    purrr::map(metadata) |>
+    prepare_merged_metadata()
+
+  expect_setequal(
+    names(observed_metadata),
+    c("library_id", "sample_id", "library_metadata")
+  )
+
+  expect_setequal(
+    observed_metadata$library_id,
+    glue::glue("library-{names(sce_list)}")
+  )
+  expect_setequal(
+    observed_metadata$sample_id,
+    glue::glue("sample-{names(sce_list)}")
+  )
+  expect_setequal(
+    observed_metadata$library_metadata |>
+      purrr::map(names) |>
+      purrr::reduce(intersect),
+    c("library_id", "sample_id", "mapped_reads", "ambient_profile")
+  )
+})