diff --git a/R/convertFromBIOM.R b/R/convertFromBIOM.R
index fe0c61a5c..4e6e5f4bf 100644
--- a/R/convertFromBIOM.R
+++ b/R/convertFromBIOM.R
@@ -68,6 +68,13 @@ NULL
 #'
 #' @param file BIOM file location
 #'
+#' @param col.data a DataFrame-like object that includes sample names in
+#'   rownames, or a single \code{character} value defining the file
+#'   path of the sample metadata file (tsv). (Default: \code{NULL}).
+#'
+#' @param tree.file \code{Character scalar}. Optional path to a phylogenetic
+#'   tree. If provided, replaces any tree stored in the BIOM metadata.
+#'
 #' @param ... additional arguments to be passed to \code{convertFromBIOM}
 #'
 #' @details
@@ -111,10 +118,27 @@ NULL
 #' tse <- importBIOM(biom_file, artifact.rm = TRUE)
 #'
 #' @export
-importBIOM <- function(file, ...) {
+importBIOM <- function(file, col.data = NULL, tree.file = NULL, ...) {
     .require_package("biomformat")
     biom <- biomformat::read_biom(file)
-    convertFromBIOM(biom, ...)
+    tse <- convertFromBIOM(biom, ...)
+
+    # Load sample metadata if provided (overrides BIOM sample metadata)
+    if (!is.null(col.data)) {
+        tse <- .add_coldata(tse, col.data)
+    }
+
+    # Load/replace tree if provided
+    if (!is.null(tree.file)) {
+        if (!.is_non_empty_string(tree.file)) {
+            stop("'tree.file' must be a single character value or NULL.",
+                 call. = FALSE)
+        }
+        tree <- ape::read.tree(tree.file)
+        rowTree(tse) <- tree
+    }
+
+    tse
 }
 
 #' @rdname importBIOM
diff --git a/R/importHumann.R b/R/importHumann.R
index e008d2a28..280727cfc 100644
--- a/R/importHumann.R
+++ b/R/importHumann.R
@@ -8,6 +8,9 @@
 #' path of the sample metadata file. The file must be in \code{tsv} format
 #' (Default: \code{NULL}).
 #' 
+#' @param tree.file \code{Character scalar}. Optional path to a
+#' phylogenetic tree. If provided, the tree is attached as \code{rowTree}.
+#' 
 #' @param colData Deprecated. Use \code{col.data} instead.
 #' 
 #' @param ... additional arguments:
@@ -69,7 +72,8 @@
 #' 
 NULL
 
-importHUMAnN <- function(file, col.data = colData, colData = NULL, ...){
+importHUMAnN <- function(file, col.data = colData, colData = NULL,
+                        tree.file = NULL, ...){
     ################################ Input check ###############################
     if(!.is_non_empty_string(file)){
         stop("'file' must be a single character value.",
@@ -84,6 +88,10 @@ importHUMAnN <- function(file, col.data = colData, colData = NULL, ...){
         stop("'col.data' must be a single character value, DataFrame or NULL.",
             call. = FALSE)
     }
+    if (!is.null(tree.file) && !.is_non_empty_string(tree.file)) {
+        stop("'tree.file' must be a single character value or NULL.",
+             call. = FALSE)
+    }
     ############################## Input check end #############################
     # Humann files has these columns that goes to rowData
     rowdata_col <- c("Pathway", "Gene_Family")
@@ -95,6 +103,11 @@ importHUMAnN <- function(file, col.data = colData, colData = NULL, ...){
     if( !is.null(col.data) ){
         tse <- .add_coldata(tse, col.data)
     }
+    # Add tree if provided
+    if (!is.null(tree.file)) {
+        tree <- ape::read.tree(tree.file)
+        rowTree(tse) <- tree
+    }
     return(tse)
 }
 
diff --git a/R/importMothur.R b/R/importMothur.R
index ff6d7ab2b..f61c00e32 100644
--- a/R/importMothur.R
+++ b/R/importMothur.R
@@ -22,6 +22,10 @@
 #' 
 #' @param designFile Deprecated. Use \code{col.file} instead.
 #'
+#' @param tree.file \code{Character scalar}. Optional path to a phylogenetic
+#'   tree in Newick format. If provided, the tree is attached as
+#'   \code{rowTree}.
+#'
 #' @details
 #' Results exported from Mothur can be imported as a
 #' \code{SummarizedExperiment} using \code{importMothur}. Except for the
@@ -72,7 +76,8 @@ importMothur <- function(assay.file = sharedFile,
                         taxonomyFile = NULL,
                         row.file = taxonomyFile,
                         designFile = NULL,
-                        col.file = designFile) {
+                        col.file = designFile,
+                        tree.file = NULL) {
 
     # input check
     if(!.is_non_empty_string(assay.file)){
@@ -87,6 +92,10 @@ importMothur <- function(assay.file = sharedFile,
         stop("'col.file' must be a single character value or NULL.",
             call. = FALSE)
     }
+    if (!is.null(tree.file) && !.is_non_empty_string(tree.file)) {
+        stop("'tree.file' must be a single character value or NULL.",
+             call. = FALSE)
+    }
     
     # Reads the assay.file 
     feature_tab_and_data_to_colData <- .read_mothur_feature(assay.file)
@@ -113,10 +122,17 @@ importMothur <- function(assay.file = sharedFile,
         rownames(sample_meta) <- colnames(feature_tab)
     }
 
-    TreeSummarizedExperiment(
+    tse <- TreeSummarizedExperiment(
         assays = S4Vectors::SimpleList(counts = feature_tab),
         rowData = taxa_tab,
         colData = sample_meta)
+
+    if (!is.null(tree.file)) {
+        tree <- ape::read.tree(tree.file)
+        rowTree(tse) <- tree
+    }
+
+    tse
 }
 
 # These extra information must be added to colData. Return list of assay and 
diff --git a/man/importBIOM.Rd b/man/importBIOM.Rd
index 563768409..792e0b1bf 100644
--- a/man/importBIOM.Rd
+++ b/man/importBIOM.Rd
@@ -10,7 +10,7 @@ results}
 \usage{
 convertToBIOM(x, assay.type = "counts", ...)
 
-importBIOM(file, ...)
+importBIOM(file, col.data = NULL, tree.file = NULL, ...)
 
 convertFromBIOM(
   x,
@@ -35,6 +35,13 @@ convertFromBIOM(
 
 \item{file}{BIOM file location}
 
+\item{col.data}{a DataFrame-like object that includes sample names in
+rownames, or a single \code{character} value defining the file
+path of the sample metadata file (tsv). (Default: \code{NULL}).}
+
+\item{tree.file}{\code{Character scalar}. Optional path to a phylogenetic
+tree. If provided, replaces any tree stored in the BIOM metadata.}
+
 \item{prefix.rm}{\code{Logical scalar}. Should
 taxonomic prefixes be removed? The prefixes is removed only from detected
 taxa columns meaning that \code{rank.from.prefix} should be enabled in the
diff --git a/man/importHUMAnN.Rd b/man/importHUMAnN.Rd
index d60f75e38..2d3bfe8d2 100644
--- a/man/importHUMAnN.Rd
+++ b/man/importHUMAnN.Rd
@@ -12,6 +12,9 @@ rownames, or a single \code{character} value defining the file
 path of the sample metadata file. The file must be in \code{tsv} format
 (Default: \code{NULL}).}
 
+\item{tree.file}{\code{Character scalar}. Optional path to a
+phylogenetic tree. If provided, the tree is attached as \code{rowTree}.}
+
 \item{colData}{Deprecated. Use \code{col.data} instead.}
 
 \item{...}{additional arguments:
diff --git a/man/importMothur.Rd b/man/importMothur.Rd
index a02d04019..7f7e38801 100644
--- a/man/importMothur.Rd
+++ b/man/importMothur.Rd
@@ -10,7 +10,8 @@ importMothur(
   taxonomyFile = NULL,
   row.file = taxonomyFile,
   designFile = NULL,
-  col.file = designFile
+  col.file = designFile,
+  tree.file = NULL
 )
 }
 \arguments{
@@ -32,6 +33,10 @@ documentation. (Default: \code{NULL}).}
 \item{col.file}{\code{Character scalar}. Defines file path of
 the sample metadata to be imported. The File has to be in \code{design
   file} format as defined in Mothur documentation. (Default: \code{NULL}).}
+
+\item{tree.file}{\code{Character scalar}. Optional path to a phylogenetic
+tree in Newick format. If provided, the tree is attached as
+\code{rowTree}.}
 }
 \value{
 A