The Top Deep Linking Challenges for Your App Development

In the rapidly advancing space of mobile app development, deep linking is one of the most powerful and overlooked tools to allow for greater user engagement, higher retention and smoother user navigation. When it is working, it™s invisible; the user clicks the link and arrives where they expected to arrive, inside an app or a place to install one. But when it doesn™t? The UX falls apart. You are losing conversions, you are breaking engagement flows, and you are creating friction that hurts trust and retention.

But most app developers and marketers are still not familiar with deep link fixing, deferred deep linking, and universal link practices. As apps become platforms for everything from fintech and social media to e-commerce, deep linking is becoming the meme of app engagement. But these also have major difficulties, such as barriers to implementation, behavior that is specific to the OS, and inconsistent behavior of links.

This article addresses most of the pain points with deep linking, app link debugging strategies, and some proven deep linking solutions so that developers can take control again and provide seamless experiences for users on the Android and iOS ecosystems.

The Value of Deep Linking in 2025

First and foremost is the obvious: users want immediacy. One Branch.io study discovered that deep linking users to specific in-app content, as opposed to simply sending them to the home page, tripled the conversion rate.

The AppsFlyer stats confirm this with deep links showing 2x retention and 25% more total session time. No matter what platform you are developing for, Android or iOS, having contextual, natural navigation is imperative.

Yet, developers still encounter significant challenges, including:

- Android and iOS inconsistencies

- Improper implementation of Android App Links

- App indexing deep link issues

- Issues with deep-linking security

- Failures of deferred deep linking in install flows

Let™s get into these issues and how the data supports solutions.

1. Challenge: Broken Deep Links After App Updates

Link breakage due to app updates is one of the most frequent deep-linking nightmares. One common issue is that developers inadvertently break URI schemes or route mappings without realizing it, resulting in broken links that do not generate any errors.

Solution: Use Universal Links and Android App Links Consistently

Universal Links for iOS and Android App Links are preferable over custom URI schemes since they are verified and controlled by the operating system. If configured correctly, they remain functional even after the app updates. For sustainability:

- On iOS, use the apple-app-site-association (AASA) file and ensure it is served via HTTPS.

- For Android, the verification consists of a JSON statement on your website.

- Running regular automated tests using Link Checker by Branch or Firebase App Distribution can allow you to catch broken links before users do.

2. Challenge: Deferred Deep Linking Failure

Deferred deep linking allows users to click a link, download the app, and be directed to the intended content after installation. This is especially important for growth campaigns and influencer marketing.

But one of the marketers™ frustrations is that this flow is not consistent, particularly for Android.

Solution: Robust Attribution Tools + First-Open Logic

Use SDKs from tools like Adjust, AppsFlyer or Branch to forward metadata with the install intent. Merge this within-app first-open logic to identify and process the deferred link data.

For Android, make sure you are implementing the Google Play Install Referrer API in order to receive install source data. Also see: Mismatches in timing (referrer data not yet available), Unmatched intent-filter declarations, Improper falling back

3. Challenge: Security Concerns with Deep Linking

Deep linking exposes entry points to your app, and with it, security risks. Deep links can also be exploited by malefactors to trigger undesired actions such as spoofed login pages, payment flows, etc.

Solution: Implement Deep Linking Security Best Practices

- Whitelist only valid hosts and strictly sanitize incoming parameters.

- Confirm app links (AASA for iOS, DAL for Android).

- Perform an in-app security gate or require reauthentication before acting, for sensitive flows (e.g., payments).

- Don™t assume link parameters are what they seem when it comes to important user actions.

In a NowSecure report, it was noted that 68% of applications supporting deep linking presented at least a œsingle bad parameter sanitization flaw. Make sure your app isn™t one of them.

4. Challenge: Poor Android App Links Optimization

Developers still misconfigure the intent filters in the Android manifest even in 2025. This sometimes causes the behavior to be erratic, some users open the app while others in the browser.

Solution: Follow Android App Links Best Practices

- Set autoVerify to true in your Android Manifest.

- Do not declare multiple intent filters for a single link domain.

- Make sure you are hosting and verifying your DAL JSON file properly.

- Use the App Links Assistant as a validation tool during development.

Of course, testing across various hardware manufacturers and Android OS versions is necessary because of Android™s fragmentation. What works on Samsung Android 13 may not work on Xiaomi Android 12.

5. Challenge: App Indexing Not Working

App indexing enables your deep-linked content to show up in search results, enhancing visibility and re-engagement. But many developers are losing out because of misconfigured app/site associations.

The Solution: Correct Setup of App Indexing Deep Links

For iOS, implement NSUserActivity and set the eligibleForSearch and eligibleForPublicIndexing flags.

- For Android you should also associate your site and your app in Google Search Console and use rel=alternate to identify content that is exclusively in the app.

- Use schema.org markup so that Google will recognize your content that is within the app.

Also, remember to check your indexing with Google™s URL Inspection Tool, Apple Search API Debugger, etc.

6. Problem: Routing Logic Across Campaigns is Complicated

The routing behavior for every entry point, if running multiple campaigns, organic, paid, referral, becomes somewhat complicated to handle. A link clicked in a WhatsApp group, for instance, should not function the same as a link clicked from a Facebook ad.

The Solution: Smart Routing and Link Personalization

Use intelligent deep linking solutions such as Branch, Kochava or Firebase Dynamic Links, that offer context-based redirects. They enable:

- Source, platform, and user status conditional redirects

- Customizing the onboarding flows

- Tracking of UTM parameters

These platforms also assist in correcting broken deep links at the moment, minimizing user drop-off as a result of deep-linking problems.

7. Challenge: Low Engagement After Initial Click

You constructed your backlinks. You have routed users correctly. However, they rebound soon after hitting the ground. Why?

In most instances, they end up in the correct destination, only not know what to do next, or the information does not meet their expectations.

Solution: Optimize Onboarding and Post-Link Experience

The moment the users arrive at the app, they need a close tie-up on the experience and the purpose of the link. This includes:

- In-depth onboard (e.g. pre-filled carts, tailor-made displays)

- Add to the app a visual connection. The design should feature a visual connection between the ad and the app.

- Micro-copy or modals which understand the starting point of the trip

According to Localytics, apps with personalized post-deep link onboarding experience up to 3x lift in retention.

Conclusion

Deep linking on the mobile is not optional anymore. It is a strategic device for growth, retention, and monetization. However, many teams merely consider it a side issue.

Developers need to be able to create apps that are quite modernized and easy to interact with to create mobile applications that are really engaging. They should know how to work with the specifics of universal links, Android App Links optimization, app indexing deep links, and details of deferred deep linking. They now need to address the toughest deep linking security, constantly track broken deep links, and smart routing that dynamically responds to the user in real-time.

In 2025 and further, it is higher. Relevance, immediacy and frictionless are what users expect. The groups that fulfil those expectations, by fixing deep linking once again, will not only keep users. They will make them become loyal ambassadors.