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Why are my transactional emails going to the junk folder and what can I do about it?

Matthew Whittaker profile picture
Matthew Whittaker
Co-founder & CTO, Suped
Published 29 Jul 2025
Updated 17 Aug 2025
7 min read
It is incredibly frustrating when transactional emails, which are critical for user experience, end up in the junk or spam folder. These aren't marketing blasts, but essential communications like password resets, order confirmations, or two-factor authentication codes. When these emails fail to reach the inbox, it directly impacts customer trust and business operations.
The good news is that while email deliverability can be complex, understanding the common reasons why your transactional emails are being flagged as spam and implementing the right solutions can significantly improve your inbox placement. I'll outline the key factors at play and provide actionable steps to help ensure your important emails get where they need to go.

Sender reputation: The foundation of deliverability

One of the most significant factors determining if your emails land in the inbox or the junk folder is your sender reputation. This reputation is essentially a trust score assigned to your sending IP address and domain by mailbox providers like google.com logoGoogle and outlook.com logoOutlook. A poor reputation, whether for your domain or IP, can swiftly lead to email filtering, causing your transactional emails to go to spam (or a blacklist). You can learn more about this in our guide to understanding email domain reputation.
Your reputation is built over time based on various metrics. Positive interactions, such as recipients opening and clicking your emails, or moving them from the junk folder to their inbox, boost your score. Conversely, negative actions like recipients marking your emails as spam, high bounce rates, or sending to spam traps (also known as honeypots) can severely damage your standing. A sudden increase in spam complaints or bounces can trigger filters, leading to immediate blocklist (or blacklist) placement. Sometimes, past behavior can also haunt your deliverability, as detailed in this Mailgun article on avoiding the spam folder.

IP reputation

Traditionally, IP reputation was paramount. If your dedicated IP (or a shared IP you used) was associated with spam, your emails would suffer. Consistent sending volume and good practices were essential for building and maintaining a positive IP reputation.
  1. Shared IPs: Reputation is influenced by all senders using the same IP, making it unpredictable.
  2. Dedicated IPs: You have full control, but it requires careful management and consistent sending volume.

Domain reputation

Today, domain reputation has gained significant importance. Mailbox providers increasingly focus on the reputation of the domain in your 'From' address. This means even if you're using a shared IP, your domain's health can largely dictate your deliverability.
  1. Consistency: Using your own domain for authentication and click tracking is crucial for building its reputation.
  2. Alignment: Proper alignment between your sending domain and authentication records is essential for deliverability.

Authentication protocols: Your first line of defense

Even with a stellar sender reputation, if your emails aren't properly authenticated, they're likely to be treated as suspicious. SPF (Sender Policy Framework), DKIM (DomainKeys Identified Mail), and DMARC (Domain-based Message Authentication, Reporting, and Conformance) are the three pillars of email authentication. These protocols help mailbox providers verify that an email truly came from your domain and hasn't been tampered with. For a comprehensive overview, refer to our simple guide to DMARC, SPF, and DKIM.
Without proper SPF records, mail servers can't easily confirm that your sending IP is authorized to send email on behalf of your domain. Missing or misconfigured DKIM signatures mean that the email's content could have been altered in transit, or it could be a spoofed message. DMARC builds upon these, giving you the power to tell mailbox providers what to do with unauthenticated emails, such as quarantining them or rejecting them outright. If your transactional emails are landing in spam despite passing all authentication checks, you may want to dive into this article on Outlook junk folders.

Example DMARC record

A basic DMARC record telling receiving servers to monitor traffic and send reports to dmarc@yourdomain.com. Setting up DMARC monitoring is essential for gaining visibility into your email authentication status and identifying issues.
DNS TXT Record for DMARCDNS
v=DMARC1; p=none; rua=mailto:dmarc@yourdomain.com; ruf=mailto:dmarc@yourdomain.com; fo=1;

Content and engagement: What recipients see and do

Even with perfect authentication, the actual content of your transactional emails and how recipients interact with them play a huge role. Mailbox providers analyze email content for characteristics often associated with spam, such as overly promotional language (even in transactional emails), suspicious links, or certain formatting. They also heavily weigh recipient engagement signals.
Transactional emails are expected to be concise, relevant, and timely. If your transactional email content is too wordy, includes marketing elements, or has vague subject lines, it can confuse spam filters and recipients alike. Recipient engagement (or lack thereof) can also tank your reputation. If users consistently ignore your emails, delete them without opening, or move them to junk, it signals to mailbox providers that your mail isn't valuable, increasing the likelihood of future filtering. Mailbox providers, including microsoft.com logoMicrosoft, interpret lack of positive engagement as a negative signal.
To troubleshoot deliverability, check your email content for spam trigger words and ensure your transactional emails are purely functional. Make it easy for users to recognize your emails and act on them positively, which means clear subject lines and calls to action. Overly flashy HTML, large fonts, or blinking text can also raise flags, according to this Namecheap article.

Category

Common phrases

Impact

Overly promotional
“Buy now,” “limited-time offer,” “free money”
Signals marketing, not transactional, content.
Vague subject lines
“Your update,” “Important information”
Recipients might ignore or mark as spam due to uncertainty.
Misleading sender names
Generic company name instead of specific service
Can lead to distrust and higher junk rates.
Excessive attachments
Unnecessary files, even small ones
Can trigger spam filters looking for malware.

List hygiene and recipient behavior

The quality of your recipient list directly affects your deliverability. Sending to unengaged or invalid email addresses can significantly harm your sender reputation and lead to your transactional emails landing in the junk folder. Mailbox providers use various mechanisms, like spam traps (also known as honeypots), to identify senders with poor list hygiene.
Spam traps are email addresses specifically set up to catch spammers. If you send emails to one, it's a strong indicator that your list is either old, purchased, or not properly maintained, leading to immediate blacklisting (or blocklisting) and severe reputation damage. Similarly, sending to inactive users who haven't opened or clicked your emails in a long time can lead to low engagement, which negatively impacts your sender score and increases the likelihood of being marked as spam or junk. This is why removing inactive users is crucial.
To prevent these issues, regularly clean your email lists by removing invalid or inactive addresses. Implement double opt-in for new subscribers to ensure they genuinely want your emails. For transactional emails, this might involve verifying email addresses at the point of sign-up or purchase. This helps maintain a high-quality list, which in turn improves your engagement metrics and signals to mailbox providers that you are a legitimate sender.

Understanding Microsoft's SCL score

Sometimes, emails to microsoft.com logoMicrosoft (Outlook, Hotmail, Live, MSN) can exhibit peculiar behavior. You might send two identical transactional emails minutes apart to the same recipient, with the first landing in junk (e.g., SCL=5) and the second in the inbox (e.g., SCL=1). This inconsistent behavior, where even Microsoft's own promotional emails occasionally hit junk, suggests that their filtering can sometimes be highly dynamic and potentially influenced by initial recipient interaction rather than just content or static reputation. While Microsoft has deprecated SmartScreen filters, the SCL (Spam Confidence Level) and BCL (Bulk Complaint Level) scores are still actively maintained and influence deliverability, as detailed in Microsoft's own documentation.
The X-Message-Delivery header in Microsoft emails provides technical details that can shed light on why an email was routed to the inbox or junk folder, including if a user's “never put this user in junk” setting is active (often resulting in an SCL of -1). This indicates that individual user preferences and interactions can override content-based filtering for subsequent emails. If your emails are consistently hitting the junk folder on hotmail.com logoHotmail, consider exploring this phenomenon further with our dedicated guide on fixing deliverability issues.

Prioritizing inbox delivery for transactional emails

Ensuring your transactional emails reach the inbox is fundamental for any business. It requires a holistic approach that considers technical configurations, content quality, and recipient engagement. By focusing on building and maintaining a strong sender reputation through proper authentication, relevant content, and diligent list management, you can significantly improve your email deliverability.
Regularly monitoring your email performance, paying attention to bounce rates and spam complaint rates, and utilizing tools to check your domain and IP against blacklists (or blocklists) are crucial steps. A proactive approach will help you identify issues early and keep your transactional emails out of the junk folder, ensuring they serve their vital purpose.

Views from the trenches

Best practices
Ensure strong authentication protocols: Implement SPF, DKIM, and DMARC for your sending domain, including proper alignment, to verify sender legitimacy and prevent spoofing. Regularly verify that your SPF, DKIM, and DMARC records are correctly set up and pass checks.
Segment infrastructure for transactional emails: If you send both marketing and transactional emails, consider separating them onto different sending IPs or subdomains to protect the reputation of your critical transactional stream.
Prioritize user engagement: Encourage positive interactions by ensuring your emails are clear, timely, and expected. When possible, prompt users to add you to their safe sender list.
Maintain pristine list hygiene: Regularly clean your recipient lists, remove inactive users, and avoid sending to old or unverified email addresses to prevent hitting spam traps or generating high bounce rates.
Use clear and concise content: Keep transactional emails focused on their primary purpose, avoiding any promotional language, unnecessary attachments, or excessive formatting that could trigger spam filters.
Common pitfalls
Over-reliance on shared IP reputation: Assuming shared IPs will always maintain good deliverability, overlooking the need for strong domain reputation and content quality.
Ignoring subtle engagement cues: Not realizing that recipients simply ignoring emails or not moving them from junk can negatively impact overall sender reputation over time.
Using a single domain for all sending: Having all email types (marketing, transactional, cold) share the same domain reputation, risking all streams if one performs poorly.
Lack of DMARC monitoring: Not using DMARC reports to identify authentication failures, SPF/DKIM misconfigurations, or potential spoofing attempts that impact deliverability.
Sending to unengaged users: Continuing to send transactional emails to inactive recipients, which degrades engagement metrics and signals low value to mailbox providers.
Expert tips
Focus on the full identity matrix: Mailbox providers evaluate a combination of IP, SPF, DKIM, and the 'From' domain. All elements contribute to your reputation and must be healthy.
Understand that every part of an email has reputation: Not just the primary sending IP or domain, but also content, URLs, and any included brands can impact deliverability.
Inconsistent SCL scores are common with Microsoft: Don't get fixated on minor fluctuations in Microsoft's SCL scores, as they can sometimes appear random. Focus on improving overall reputation and user engagement.
Domain reputation often outweighs IP reputation: While both are crucial, domain reputation is increasingly becoming the more dominant factor in deliverability decisions, especially for authenticated mail.
Encourage users to move emails out of junk: Mailbox providers, especially Microsoft, value positive user interaction like moving an email from junk to inbox. This action provides a strong signal of legitimacy.
Marketer view
A marketer from Email Geeks says they have seen Microsoft's own replies to deliverability tickets end up in spam until manually marked as not spam in Outlook, highlighting the unpredictability of Microsoft's filters.
2024-09-26 - Email Geeks
Expert view
Expert Laura from Email Geeks says that if users do not engage positively by interacting with an email, it will hurt the sender's reputation and contribute to spam folder placement for other recipients.
2024-09-26 - Email Geeks

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    Why are my transactional emails going to the junk folder and what can I do about it? - Sender reputation - Email deliverability - Knowledge base - Suped