diff --git a/.ci/lint_r_code.R b/.ci/lint_r_code.R
index c13471ca8fb1..12116104ef6d 100755
--- a/.ci/lint_r_code.R
+++ b/.ci/lint_r_code.R
@@ -33,29 +33,37 @@ LINTERS_TO_USE <- list(
     , "any_duplicated"       = lintr::any_duplicated_linter()
     , "any_is_na"            = lintr::any_is_na_linter()
     , "assignment"           = lintr::assignment_linter()
+    , "boolean_arithmetic"   = lintr::boolean_arithmetic_linter()
     , "braces"               = lintr::brace_linter()
     , "class_equals"         = lintr::class_equals_linter()
     , "commas"               = lintr::commas_linter()
     , "duplicate_argument"   = lintr::duplicate_argument_linter()
+    , "empty_assignment"     = lintr::empty_assignment_linter()
     , "equals_na"            = lintr::equals_na_linter()
+    , "for_loop_index"       = lintr::for_loop_index_linter()
     , "function_left"        = lintr::function_left_parentheses_linter()
     , "implicit_integers"    = lintr::implicit_integer_linter()
     , "infix_spaces"         = lintr::infix_spaces_linter()
     , "inner_combine"        = lintr::inner_combine_linter()
+    , "is_numeric"           = lintr::is_numeric_linter()
     , "fixed_regex"          = lintr::fixed_regex_linter()
+    , "function_return"      = lintr::function_return_linter()
+    , "lengths"              = lintr::lengths_linter()
     , "literal_coercion"     = lintr::literal_coercion_linter()
     , "long_lines"           = lintr::line_length_linter(length = 120L)
+    , "matrix"               = lintr::matrix_apply_linter()
     , "missing_argument"     = lintr::missing_argument_linter()
-    , "no_tabs"              = lintr::no_tab_linter()
     , "non_portable_path"    = lintr::nonportable_path_linter()
     , "numeric_leading_zero" = lintr::numeric_leading_zero_linter()
     , "outer_negation"       = lintr::outer_negation_linter()
     , "package_hooks"        = lintr::package_hooks_linter()
     , "paste"                = lintr::paste_linter()
+    , "quotes"               = lintr::quotes_linter()
+    , "redundant_equals"     = lintr::redundant_equals_linter()
     , "regex_subset"         = lintr::regex_subset_linter()
+    , "routine_registration" = lintr::routine_registration_linter()
     , "semicolon"            = lintr::semicolon_linter()
     , "seq"                  = lintr::seq_linter()
-    , "single_quotes"        = lintr::single_quotes_linter()
     , "spaces_inside"        = lintr::spaces_inside_linter()
     , "spaces_left_parens"   = lintr::spaces_left_parentheses_linter()
     , "sprintf"              = lintr::sprintf_linter()
@@ -96,9 +104,11 @@ LINTERS_TO_USE <- list(
             , "??" = interactive_text
         )
     )
-    , "unneeded_concatenation" = lintr::unneeded_concatenation_linter()
-    , "unreachable_code"       = lintr::unreachable_code_linter()
-    , "vector_logic"           = lintr::vector_logic_linter()
+    , "unnecessary_concatenation" = lintr::unnecessary_concatenation_linter()
+    , "unnecessary_lambda"        = lintr::unnecessary_lambda_linter()
+    , "unreachable_code"          = lintr::unreachable_code_linter()
+    , "vector_logic"              = lintr::vector_logic_linter()
+    , "whitespace"                = lintr::whitespace_linter()
 )
 
 noquote(paste0(length(FILES_TO_LINT), " R files need linting"))
diff --git a/.ci/test.sh b/.ci/test.sh
index 665e7f6546ec..b3acc4a670cf 100755
--- a/.ci/test.sh
+++ b/.ci/test.sh
@@ -73,7 +73,7 @@ if [[ $TASK == "lint" ]]; then
         cpplint \
         isort \
         mypy \
-        'r-lintr>=3.0' \
+        'r-lintr>=3.1' \
         ruff
     source activate $CONDA_ENV
     echo "Linting Python code"
diff --git a/R-package/R/lgb.interprete.R b/R-package/R/lgb.interprete.R
index e0de0b781079..7de772664d8b 100644
--- a/R-package/R/lgb.interprete.R
+++ b/R-package/R/lgb.interprete.R
@@ -72,7 +72,9 @@ lgb.interprete <- function(model,
   leaf_index_dt <- data.table::as.data.table(x = pred_mat)
   leaf_index_mat_list <- lapply(
     X = leaf_index_dt
-    , FUN = function(x) matrix(x, ncol = num_class, byrow = TRUE)
+    , FUN = matrix
+    , ncol = num_class
+    , byrow = TRUE
   )
 
   # Get list of trees