Using Microsoft Graph for Custom App Integrations

You’ve automated a workflow with Microsoft 365, only to hit a
wall with constant permission requests, broken background jobs,
and security warnings. Why do custom app integrations feel so
much riskier than they should? Today, I’m breaking down the
hidden security traps of delegated permissions—and the smarter
path almost nobody talks about: app-only permissions in Microsoft
Graph.If you want safer, smoother Microsoft 365 integrations that
just work, stick around. We’ll tackle exactly where most setups
go wrong, and I’ll show you the step-by-step fix that unlocks
seamless, secure automation.


Why Delegated Permissions Break Your Automation


If you’ve ever found yourself wondering why your Microsoft 365
automations stall out at the worst possible time, you aren’t
alone. Maybe it’s late at night. You’ve set up Power Automate to
sync files for accounting, and you think you’re set—but two hours
later, that job throws a “please login” prompt or just quietly
dies while nobody’s watching. The reason? Most custom apps and
automations start with delegated permissions, because—honestly—it
feels like the quickest way to get something working. Use a
user’s credentials, check a box, and your app instantly inherits
whatever that person can do. For a new project, that approach is
often tempting. It’s practically encouraged by the UI when
setting up flows, bots, or even one-off scripts.But there’s a
catch that comes back to bite every single admin who tries to
scale this model. Delegated permissions tie your automation to an
actual human user. Under the hood, every API call is piggybacking
on a real person’s permissions and session. That means anytime
the user logs out, gets a new password, or leaves the company,
your critical workflow grinds to a halt. The job doesn’t just hit
pause; it fails—sometimes loudly with an error, sometimes in
silence until someone starts asking about missing reports.Wake up
calls usually come early. One morning you discover that automated
file upload you tested for weeks suddenly failed at 2 AM. Support
tickets pile up. The logs just show “authentication failed,” or
sometimes nothing at all because a session silently expired. It’s
not just about the inconvenience, either. There’s research
showing that 70 percent of custom Microsoft 365 app support
tickets boil down to issues with authentication and token
handling—not the logic of the app itself. Most of those relate
directly back to delegated permissions: session timeouts, invalid
tokens, or missing MFA steps.It sneaks up on you in other ways,
too. Delegated permissions are persistent headaches when users
change roles or go out on leave. Your payroll bot or HR
automation? Relying on an account tied to a real person is an
accident waiting to happen. Even if you assign a special “service
account,” someone’s going to forget the password expiration, or
not realize the license is about to be removed. Internal audits
end up flagging flows and bots that haven’t run in weeks because
nobody even checked that a password needed updating.What’s worse
is that the path of least resistance encourages risky shortcuts.
Maybe your workflow needs to touch resources across SharePoint,
Exchange, and Teams. You keep adding permissions to “make things
work”—a little more mailbox access here, site collection access
there, until suddenly the user tied to that process has more
admin rights than your own IT staff. For the sake of reliable
automation, teams sometimes grant global admin status to these
accounts. Not because it’s smart, but because delegated
permissions force your hand when automation becomes
business-critical. That transfer of privilege isn’t
theoretical—there are plenty of real-world stories about bots
accidentally gaining far too much access because delegated
accounts kept hitting permission errors.The cracks keep adding
up. Let’s say you run a monthly reconciliation process for
Finance. Every month, the Power Automate flow slows down—or
worse, fails outright. Why? It depends on a single delegated
account that loses its session, has its password changed, or gets
flagged by security. Then, a Teams notification pings your admin
on a Sunday morning, or a finance report doesn’t get delivered.
Fixing these issues isn’t just tedious—it chips away at your
confidence in automation altogether. Suddenly, you have to ask
yourself: is the time you saved with automation just spent
troubleshooting all the new failure points?It gets messier as
your organization grows. Scheduled SharePoint syncs, background
tasks for compliance archiving, automated chatbots serving HR
questions at odd hours—all of them end up teetering on the
stability of whichever user account is backing the permissions.
Unlike true service principals, users get deprovisioned, their
accounts age out, sometimes they leave, and IT is left picking up
the pieces. When everything is built on a stack of delegated
permissions, small changes in personnel or security policy ripple
out and break things you didn’t even realize depended on that one
login.On top of the technical pain, there’s always an
uncomfortable conversation with Security. If you’re giving broad
delegated rights “just to make it work,” you’re setting up a
situation where a breach in that single user account compromises
not just their inbox, but anything your automated job can
touch—in some cases, the entire directory. Mistakes compound. If
you’ve got critical reports or financial automations tripping
over password resets or license removals, your stakeholders start
to ask if automation is worth the risk at all.The frustrating
part is that none of this is particularly rare or new. In
practice, a massive percentage of custom Microsoft 365
automations fail or stall because delegated permissions seemed
easy at first, but break down in anything resembling a real-world
scenario. A single user’s password prompt shouldn’t be enough to
stop payroll from running or compliance jobs from archiving
emails. Yet, that’s often exactly what happens. It’s death by a
thousand cuts, and the more ambitious your automation, the more
these issues cost you both in time and in security risks.So, if
delegated permissions have you managing user accounts like a
house of cards, it’s not just you. For service accounts,
background jobs, and any workflow that should “just work” without
a user present, there’s a better way hiding in plain sight. The
question is: are you ready for the approach that actually
supports secure, reliable automation—without babysitting logins?


Solving the Maze: How App-Only Permissions Change the Game


So here’s what most IT pros wish someone had told them sooner—big
organizations don’t gamble critical automations on a user’s
password or session lasting the night. They use app-only
permissions. It’s not because they have more resources or buy
some super-premium Microsoft license. The difference is in how
their apps talk to Microsoft Graph: not as Jane from HR, or Tim
from Finance, but as a dedicated application identity. This
approach means the app itself is recognized as its own entity in
Azure AD. No one needs to log in. No one’s credentials go stale.
If you need a SharePoint job to run at 3 AM, it doesn’t check if
someone’s sitting at their desk—it just works.App-only
permissions are kind of the secret sauce behind reliable
automation. Once you get this concept, things actually get
simpler. The app gets a defined set of permissions—say, access to
just the resources it needs on SharePoint, Teams, or
Outlook—nothing more. That’s the principle of least privilege in
action. Instead of a bot inheriting every permission tied to a
specific user (and all the risk that comes with it), your app
only gets the exact access it needs to do its job. You get more
predictability in what it can access, less exposure if something
goes sideways, and no headaches chasing down that elusive “global
admin” checkbox just to keep automation running overnight.But
here’s why the idea is both powerful and, for most, intimidating:
setting up app-only permissions doesn’t come with a one-click
button labeled “make this secure and easy.” The interface is
scattered across Azure AD, the Graph Portal, and sometimes even
the classic legacy admin pages. Registering an app means
navigating menus, picking an authentication method, setting the
right callback URLs, and ultimately picking permissions out of a
dropdown that’s definitely longer than it needs to be. There’s
nowhere in the process that stops and explains why some
permissions are labeled “Application,” others “Delegated,” or
what happens if someone grants too much access. Most tutorials
gloss over the messy middle. You’ll see quick demos of setting up
client secrets or certificates—but almost none show the aftermath
when the wrong permission is selected, or the admin consent
process goes sideways.Every admin knows the feeling: you think
you’ve set everything up, but the next step throws you a cryptic
error. Maybe “Insufficient privileges” pops up when you test the
Graph call, or your webhook refuses to fire because consent
wasn’t properly granted. Figuring out why can turn into a support
ticket scavenger hunt. When you finally track it down, it’s
something like “Application not authorized by admin,” which
translates to: someone needs to give organizational-level consent
before this app can act without a user present. Depending on your
tenant’s security policies, that step might involve layered
approvals or even a change management process.Let’s play out what
happens when you get it right. Your app is now its own service
principal. Want to upload documents to SharePoint, even if
everyone’s offline or accounts are in limbo? No problem—the bot
has the permissions and it never gets kicked out for inactivity.
Say you’re running a nightly archive of conversations from Teams
to SharePoint for compliance. People can switch jobs, leave the
company, or just forget their password over the holidays—your
automation keeps running as if nothing changed. Think about what
that means for scale. Suddenly, you can line up hundreds of
process automations or reporting tasks without having to assign a
Frankenstein set of permissions to service accounts that confuse
both admins and auditors.One real-world example: A large
insurance provider built a document processing bot that ingests
daily reports, uploads files to SharePoint, and sends alerts if
something looks off. No delegated access, no dependency on a
user—just app-only permissions mapped to exactly what’s in scope.
The bot ran for months before its secret expired (and yes, they
set a calendar reminder for that). Not one ticket about failed
authentication, not one Teams ping at three in the morning. It
wasn’t luck—it was by design.Microsoft, for its part, leans into
this hard in their documentation. Their guidance is clear: if
you’re building background services or automating tasks that
aren’t tied to a logged-in user, use app-only permissions.
“Reduced attack surface and easier auditing”—that’s not just
marketing. It makes log analysis and compliance reviews cleaner
because you know exactly what the app can and can’t do. If
something goes wrong, you aren’t left wondering which user’s
session triggered a problem. Every action’s tied back to the
app’s identity, not a person.Of course, app-only permissions
don’t mean you throw out best practices. You still need to be
smart about which specific permissions you select. Less is more.
Only check the boxes your automation actually needs—write access
for that one site, maybe, but not “Full control of all SharePoint
sites” unless there’s no alternative. This narrows any risk if a
secret leaks or if someone else tries to elevate permissions for
convenience later. It’s the opposite of the “give it global
admin, just to get it working” shortcut everyone regrets.There’s
a practical payoff to this shift beyond just fewer support
tickets. When you cut out all the dependency on user accounts,
your automations become more resilient—not just to session
timeouts, but to org changes, onboarding, offboarding, and even
licensing surprises. You’re free to build workflows and bots that
survive employee turnover, role changes, or surprise security
updates.So, what does it take to actually set this up without
getting lost in permissions hell? Registration, permissions,
consent, and securing your secrets—the steps matter, and missing
any one of them can land you right back at square one. Next, I’ll
lay out the specific moves you need to make to set up app-only
permissions properly, dodge the common failure points, and
actually get the benefits everyone promises but few deliver in
their guides.


Step-by-Step: Setting Up App-Only Permissions Without the Gotchas


If you’ve ever paced through Azure AD’s endless panels and still
wound up staring down a “403 Insufficient privileges” message,
welcome to the club. The registration process for app-only
permissions isn’t just unnecessarily complex—it’s filled with
silent traps. Most “getting started” blogs make it sound like a
two-minute checklist, but if you’ve tried doing it in production,
you know how easy it is to get all the way through and still miss
the one tiny box that makes everything break. What’s worse, the
UI doesn’t always tell you what’s missing. One misplaced
permission or a skipped consent page, and you’ll be
troubleshooting for the rest of the afternoon, or worse, pushing
changes to production and hoping for the best.Let’s talk about
those gotchas that no one highlights until you’re neck-deep in
failed runs. Step one is registering your app in the Azure
portal. You click “New registration,” give your app a sensible
name (or something you’ll immediately regret in a week), and move
to the redirect URIs. Most background services don’t need these,
so you skip over it, but sometimes skipping it means your app
throws errors down the road—with no clear link to what went
wrong. The core catch is in the permissions setup. The default is
to assign “Delegated” permissions, since that’s what most
user-facing apps need. But for background processes, you
absolutely need to switch to “Application” permissions. The
difference isn’t just academic—Delegated permissions assume a
user is involved, while Application permissions let the app
itself act as a first-class citizen.The list of permissions is
massive, and easy to get lost in. Maybe your automation just
needs access to upload to a specific SharePoint document
library—but if you choose “Sites.Read.All” instead of
“Sites.FullControl.All,” you’ll see cryptic errors about missing
privileges, even though in the portal it looks fine. The trick is
to map exactly what your workflow needs, nothing more.
Over-provisioning seems tempting when you hit a weird error, but
it just increases your risk later, making audits a nightmare. At
this step, take a breath and actually read what each permission
grants—because you’ll need to justify that list to Security, if
not right away, then at your next annual review.Now comes the
true test: admin consent. Even if you pick the right permissions,
the permissions don’t mean anything until an admin grants
consent. Depending on your tenant’s policies, this can range from
a one-click accept to a week-long approval process. Some
organizations have layered consent controls, so your request
bounces around, and meanwhile, the UI tells you everything is
ready. Spoiler: it’s not. The symptom everyone hits here is
running your app and seeing “Insufficient privileges”—not because
you didn’t add the permission, but because the admin didn’t
finalize consent on the backend. Double-checking consent in
Enterprise Apps > Permissions is always worth the time, even
if the dashboard claims you’re all set.Let’s not gloss over
securing your credentials. After you register the app, you
generate a client secret. Here’s where a lot of folks cut
corners—storing the secret in plain text with the code, or
tossing it somewhere on a shared drive. That secret is your app’s
identity card for Microsoft Graph, and exposing it even briefly
is an open door for attackers. Always store secrets in a secure
vault—Azure Key Vault if possible—and set a reasonable expiration
date. Long-lived secrets sound convenient until the day you
forget to rotate one and your automation grinds to a halt after
nine months because of an expired credential. Rotate proactively,
log reminders, and make “least privilege” the default mindset for
both secrets and permissions.There’s another, less-advertised
wrinkle with error handling. App-only permissions surface errors
differently than delegated ones. For example, if you’re testing a
file upload bot for SharePoint, missing access means you’ll get
back a dry “insufficient privileges” from the Graph API—no
hand-holding from the UI, no “missing user context.” You need to
be ready to parse that error detail and know exactly which
permission it maps to. The only way to debug cleanly is by
running consent and access checks for each scope in your
pipeline.Take that file upload bot as a real-world example. You’d
start by registering your app, picking “Application” permissions
for SharePoint, and requesting “Sites.ReadWrite.All” only if
absolutely necessary. Once admin consent is granted, you generate
a client secret, lock it down, and plug it into your automation’s
configuration. The first run? You’ll probably see a cryptic
error—maybe a GUID or a “Resource not found.” Almost always, it’s
a mismatch between the library your app is calling and the
permission assigned. The learning curve here is real, but once
you work through the exact SharePoint site ID, URL mapping, and
permission scope, suddenly your bot uploads files at 2 AM, no
user needed. The logs fill with clean success messages, not error
dumps.The key takeaway: every detail in the process matters.
Register the app, pick only Application permissions, secure and
regularly rotate your secrets, and confirm admin consent actually
went through. Get this chain right, and your automation becomes
both safer and almost completely self-sufficient. Your support
tickets drop, security has fewer questions, and you have more
confidence handing off support duties to the next team member—a
win all around.Now that you’ve finally got app-only permissions
lined up and running strong, the natural next step is pushing
those limits: real-time notifications, bi-directional updates,
and integrating with more live Microsoft 365 features. That’s
where webhooks and modern toolkits can really expand your
automation landscape, if you know the quirks ahead of time.


Automation in Action: Real-World Benefits and Live Notifications


Imagine running an app that quietly keeps the wheels turning
while everyone else is offline. SharePoint uploads land in the
right document libraries at two in the morning, Teams alerts fire
off when a new file arrives, and dashboards keep themselves up to
date with zero manual interference. Nobody has to check in, log
on, or wonder if their account might throw a wrench in the
process. That’s the everyday reality once you’ve moved your
automation to app-only permissions. It changes what’s
possible—not just because things stop breaking when people leave
for vacation, but because you can finally trust that your
background processes will outlive any single user’s session.It’s
one thing to see basic jobs run overnight, but the reliability
goes further. Take a case where the business needs file syncs
across different SharePoint sites, Teams updates for new records,
and a management dashboard that pulls numbers every few hours.
Before app-only permissions, there’d be a real risk that some
component of the chain would go dead thanks to a missed login.
After the move, that chain hums along, regardless of who’s out
sick or whose password gets updated. You start to see those
midnight Teams pings get replaced by real, actionable
notifications, waking people up for reasons that actually
matter.Yet reliability is only half the story. Let’s talk about
scale and real-time events. With app-only permissions, you don’t
just turn on background jobs—you start plugging into events as
they happen, even with no user online. Webhooks in Microsoft
Graph become an option for actual production work, not just
developer experiments. Set up a webhook and your app can
subscribe to changes on a SharePoint site or new messages in a
Teams channel, getting a prompt nudge every time an event lands.
There’s no dependency on user presence, which means you don’t
miss a thing when staff close their laptops or go on
holiday.Setting up webhooks, though, isn’t as “set it and forget
it” as the rest of the app-only model. Microsoft Graph expects
tighter controls when there isn’t a user session. Every webhook
subscription has to be created and renewed by your app itself,
using its identity—not a random service account. During setup,
you need to prove your endpoint is legit, which means handling
the validation token Microsoft sends in the very first request.
Miss that, and your notifications never start. Endpoint security
also gets ramped up. Microsoft enforces stricter requirements on
HTTPS, and expects your receiver to be able to process
high-throughput bursts and retries without exposing confidential
details in responses.The Graph Toolkit can smooth out a lot of
the Graph API’s rough edges, but there’s a caveat. Out of the
box, many of the components assume “delegated” sign-in for
interactive user sessions. To take advantage of app-only
permissions, you need to deliberately configure components in
your own context—often calling Graph endpoints directly from your
backend, or customizing the provider logic to hand over the
app-only token. It’s a step extra, but it’s what lets you drop
those dependencies on users entirely. Care here means you’re not
trading one set of headaches for another: error scopes become
clearer, failures are logged with the correct identity, and
callbacks don’t suddenly switch context just because someone logs
in or out in the browser tab.Best practice at this point is less
about wizard-style setup and more about discipline. With app-only
permissions, failures don’t bubble up politely—the API just
returns a status code with your operation. That means logging
every failure, especially transient ones, is your first line of
defense. If your automation retries after a temporary network
issue, it should do so with exponential backoff and without
dumping secrets or tokens in a log file. Whenever a process
fails, make sure you record enough context: what operation, what
resource, and which permission may have been in play. Don’t fall
into the habit of retrying endlessly—rate limits hit hard with
app-only calls, and a single runaway process can end up locked
out for hours if it’s careless.Here’s a real scenario that brings
it all together. A Power Platform app combines SharePoint file
sync, Teams messaging, and automatic dashboard refreshes.
Everything runs headless. The data flow starts with a webhook
that lets the app know when a new document lands in SharePoint.
That triggers an app-only call to grab the file, process it, and
push metadata to a Teams channel for review. It wraps up by
updating a summary value in a company-wide Power BI dashboard. No
users were involved in any step. If someone tries to deprovision
the app, or if permissions change, everything is logged—in fact,
those events can trigger their own notifications. That’s a
feedback loop most companies have dreamed about but rarely
achieve with delegated permissions.Moving to this model changes
your support tickets, too. Fewer late night calls about expired
passwords, fewer “user not found” errors. Audit trails make more
sense, since every background job shows up as the app’s identity,
not some catch-all account. If security wants to know what
happened last Tuesday at 4 AM, you have logs tying each event to
a specific machine operation, not a mystery human.The
organizational picture shifts when automation just works. Think
less time spent debugging and more confidence when spinning up
new integrations, branching into new departments, or even
expanding across tenants. Suddenly, the “scary” parts of
automation—like live notifications and hands-off
processing—become the foundation you rely on for everything else.
That opens the door to even bigger changes for how your business
handles information and keeps people connected, no matter how
many apps you build or how fast your environment evolves.


Conclusion


If you’ve slogged through background job failures and endless
permission errors, you know why app-only permissions matter.
They’re not just a patch—they create a real foundation for
automation that actually survives org changes, policy updates,
and day-to-day churn. Instead of patching user accounts or adding
risky shortcuts, you set your automations up for the long haul.
If your goal is for custom apps to be more resilient while
reducing support overhead, now is the time to get intentional
about your permissions model. Want to keep building smarter?
Subscribe and let me know the one Microsoft 365 automation pain
point you keep wrestling with.


Get full access to M365 Show - Microsoft 365 Digital Workplace
Daily at m365.show/subscribe