During this week’s WWDC keynote, executives touted improvements to popular services like Siri, iMessage, and Apple Music. They demonstrated exciting new uses for nascent features like 3D Touch. Amid all the fuss, though, they neglected to talk much about the security measures coming to MacBooks and iPhones this fall. That’s a shame, because there are lots. And they’re going to significantly alter how you interact with your Apple devices.

While Apple appears to have delayed some of its bigger security projects—most notably, encrypting iCloud backups so that not even Apple can access them—it’s still showing serious ambition, sometimes in surprising places. The result will be an iOS and macOS experience that trades convenience for protection in a few key ways. Apple will introduce small frustrations now, to prevent large, even unfixable, frustrations down the road.

So Long, Flash (And Everything Else)

Apple’s crusade against Flash dates back to 2010, when Steve Job famously penned an open letter banishing it from the iPhone. Since then, plenty of others co-signed. Facebook’s security chief called for a Flash end-of-life date last summer, and Google has taken multiple steps to limit its viability on Chrome. Even Adobe has lately distanced itself from its most notorious product.

It took until macOS Sierra, though, for Apple to bring its Flash fight to the desktop. And in fact, it’s not stopping at Flash: the next version of Safari won’t support popular plugins like Java, Silverlight, and even Apple’s own QuickTime. But, y’know, mostly Flash. Instead, it’s embracing the much more secure HTML5 standard whenever and wherever it can.

“On websites that offer both Flash and HTML5 implementations of content, Safari users will now always experience the modern HTML5 implementation, delivering improved performance and battery life,” writes Apple’s Ricky Mondello. “This policy and its benefits apply equally to all websites; Safari has no built-in list of exceptions.”

No Flash, no exceptions—even on sites that don’t offer an HTML5 alternative. When Safari runs into sites that require Flash or any other plug-in, it will act as though the plug-in is not installed on your computer. Instead, it will show you a notice that Flash is not installed, and serve up a link to where you can download it. Only after you click that link will Safari let you know that well, actually Flash is, in fact, on board. You’ll have the option to either activate it that one time (the default) or every time that particular site is visited. Sounds annoying? Yeah, it will it be.

The newfound peace of mind, though, is worth the occasional extra click or three. Though plugins like Flash, Silverlight, Java, and QuickTime are still fairly common across the web—Amazon Video, for instance, leans on Silverlight in Safari—they are notoriously easy targets for hackers. Flash in particular is and continues to be a security nightmare; just this week, another critical vulnerability hit it, which could “allow an attacker to take control of the affected system.” So yeah, it’s more annoying for you, but extremely important for your digital well-being.

And it’s important that Apple doesn’t stop at Flash; even if and when Flash is minimized, bad actors will just move onto the next popular plug-in to cause havoc. Like, say, Java, which itself is consistently rated as one of the biggest security threats to US computers.

A Stronger Gatekeeper

Similarly, Apple’s Gatekeeper is digging a deeper moat. First introduced in 2012, Gatekeeper lets Mac users specify whether they allow their computer to download only applications from the App Store, or from the App Store as well as applications signed by certified Apple developers, or from anywhere at all consequences be damned. In macOS Sierra, that last option no longer exists.

You’ll still be able to run unsigned apps by right-clicking and selecting “Open.” Power users can also shut down Gatekeeper entirely in the terminal. But it means that most casual Mac owners wind up only using apps for whose security Apple can vouch.

Think of it like this: Your iPhone and Mac are a house, and Apple’s covering up as many outlets as it can. That’s a pain when you need to plug something in, but at least you won’t wind up electrocuted.

HTTPS All of the Apps

We’ve talked about the importance of HTTPS, and at WIRED we’ve lived it. And while it’s been encouraged in iOS before, as of next year it’s going to be mandatory for any app that connects to the web.

Apple introduced App Transport Security, which makes sure apps are using encrypted HTTPS connections whenever they access web services, last year. And to be fair, a lot of developers have already boarded that train. That’s partly because it’s such a relatively small ask on the part of iOS developers. “We use HTTPS across the board,” says Adam Grossman, co-founder of popular weather app Dark Sky. “The fact that Apple is enforcing this ‘best practice’ is a good thing.”

Better still, you shouldn’t see much impact in your day to day app usage. “HTTPS requires an extra ‘handshake’ between servers, and there’s a bit of a CPU overhead, but in practice this isn’t a big deal for performance in a lot of, if not most cases,” says Grossman.

There could be some performance issues that pop up, especially in an app that’s not actively tended to.

“Apps could crash when they’re launched, or ads that are served within the app could fail, neither of which is great for the overall user experience,” says Brad Wright, an executive with Phunware, a company that specializes in app development and mobile experiences. “But the likelihood of those scenarios is extremely low. The development community has had ample time to make this change.”

It’s especially important to know that apps are operating on HTTPS because there’s often no visual indicator (like the green lock icon in the upper-left corner of a desktop browser) to let users know how secure their connection is. As of January 1, 2017, they’ll all be secure, full stop. You won’t have to even think about it.

An Exciting File Management System (No, Really)

It’s hard to get hyped about a file management system. But if you were ever going to, it should be about Apple’s new APFS. There’s a ton to like here; it works across all of Apple’s platforms, supports both Flash storage and solid-state devices, and clones files rather than copies them (which should save a ton of room). Best of all, it isn’t 18 years old, like the system it will replace next year is.

That’s a quick gloss of a complicated subject, but all in the service of getting to the real bones of APFS: file-level encryption.

While full-disk encryption has been an OS X feature since 2011, APFS lets you encrypt files with single-key encryption, multi-key encryption, or no encryption at all (but don’t do that!). This is a very big deal, not just for security, but for usability.

“Apple already has FileVault encryption in software. It’s not done by the file system, it’s done by the operating system,” says Greg Norcie, staff technologist at the Center for Democracy & Technology. “In general, if you’re going to do something in software it’s going to be slower than if you do it at the file system level. It’s going to make everything more seamless.”

As for the encryption itself, on most devices APFS will use AES-XTS encryption, which Norcie notes is what’s used to protect top-secret government information.

APFS is still an early developer preview (translation: a lot of it doesn’t work yet) so it’s not quite ready for road testing unless you really know what you’re doing. When it takes over next year, though, it’s going to give you far more granular control over your security than Apple ever has before.

It’s understandable that these features didn’t make the keynote stage. They’re wonky, and technical, and don’t sound quite as cool as “differential privacy, a term that was touted on stage—which is, in fairness, actually pretty cool. In terms of how they impact your safety day to day, though, each represents serious, tangible progress. The best part? When these updates are working best, you won’t notice them at all.