diff --git a/NEWS.md b/NEWS.md
index 48fda94a..c832e132 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -20,6 +20,8 @@
 * The `renv.lock` is ignored when the `RSCONNECT_PACKRAT` environment variable
   or the `rsconnect.packrat` option is set. (#936)
 
+* The content type is inferred by analyzing the set of top-level files. (#942)
+
 # rsconnect 1.0.1
 
 * `deployDoc()` includes `.Rprofile`, `requirements.txt` and `renv.lock` when
diff --git a/R/appMetadata.R b/R/appMetadata.R
index 0a1b8234..b8cbecb5 100644
--- a/R/appMetadata.R
+++ b/R/appMetadata.R
@@ -36,7 +36,7 @@ appMetadata <- function(appDir,
     # Inference only uses top-level files
     rootFiles <- appFiles[dirname(appFiles) == "."]
     appMode <- inferAppMode(
-      file.path(appDir, appFiles),
+      file.path(appDir, rootFiles),
       usesQuarto = quarto,
       isShinyappsServer = isShinyappsServer
     )
@@ -117,7 +117,7 @@ checkAppLayout <- function(appDir, appPrimaryDoc = NULL) {
 }
 
 # infer the mode of the application from files in the root dir
-inferAppMode <- function(absoluteAppFiles,
+inferAppMode <- function(absoluteRootFiles,
                          usesQuarto = NA,
                          isShinyappsServer = FALSE) {
 
@@ -127,24 +127,24 @@ inferAppMode <- function(absoluteAppFiles,
   }
 
   # plumber API
-  plumberFiles <- matchingNames(absoluteAppFiles, "^(plumber|entrypoint).r$")
+  plumberFiles <- matchingNames(absoluteRootFiles, "^(plumber|entrypoint).r$")
   if (length(plumberFiles) > 0) {
     return("api")
   }
 
   # Shiny application using single-file app.R style.
-  appR <- matchingNames(absoluteAppFiles, "^app.r$")
+  appR <- matchingNames(absoluteRootFiles, "^app.r$")
   if (length(appR) > 0) {
     return("shiny")
   }
 
-  rmdFiles <- matchingNames(absoluteAppFiles, "\\.rmd$")
-  qmdFiles <- matchingNames(absoluteAppFiles, "\\.qmd$")
+  rmdFiles <- matchingNames(absoluteRootFiles, "\\.rmd$")
+  qmdFiles <- matchingNames(absoluteRootFiles, "\\.qmd$")
 
   if (is.na(usesQuarto)) {
     # Can't use _quarto.yml alone because it causes deployment failures for
     # static content: https://github.com/rstudio/rstudio/issues/11444
-    quartoYml <- matchingNames(absoluteAppFiles, "^_quarto.y(a)?ml$")
+    quartoYml <- matchingNames(absoluteRootFiles, "^_quarto.y(a)?ml$")
 
     usesQuarto <- length(qmdFiles) > 0 ||
       (length(quartoYml) > 0 && length(rmdFiles > 0))
@@ -167,7 +167,7 @@ inferAppMode <- function(absoluteAppFiles,
   # Shiny application using server.R; checked later than Rmd with shiny runtime
   # because server.R may contain the server code paired with a ShinyRmd and needs
   # to be run by rmarkdown::run (rmd-shiny).
-  serverR <- matchingNames(absoluteAppFiles, "^server.r$")
+  serverR <- matchingNames(absoluteRootFiles, "^server.r$")
   if (length(serverR) > 0) {
     return("shiny")
   }
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index e8d4a92a..579386bd 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -51,6 +51,10 @@ local_temp_app <- function(files = list(), env = caller_env()) {
 
   for (name in names(files)) {
     content <- files[[name]]
+    hier <- dirname(name)
+    if (!hier == ".") {
+      dir.create(file.path(dir, hier), recursive = TRUE)
+    }
     writeLines(content, file.path(dir, name))
   }
 
diff --git a/tests/testthat/test-appMetadata.R b/tests/testthat/test-appMetadata.R
index c5e44337..dbb04a1e 100644
--- a/tests/testthat/test-appMetadata.R
+++ b/tests/testthat/test-appMetadata.R
@@ -33,6 +33,13 @@ test_that("handles special case of appPrimaryDoc as R file", {
   expect_equal(metadata$appMode, "shiny")
 })
 
+# https://github.com/rstudio/rsconnect/issues/942
+test_that("files beneath the root are not ignored when determining app-mode", {
+  dir <- local_temp_app(list("app.R" = "", "plumber/api/plumber.R" = ""))
+  metadata <- appMetadata(dir)
+  expect_equal(metadata$appMode, "shiny")
+})
+
 # checkLayout -------------------------------------------------------------
 
 test_that("checkLayout() errors if primary doc & app.R", {