Your navigation menu and collection filters are doing one of two things right now… guiding your website visitors to exactly what they’re looking for, or making them work for it. And if it’s the latter, they’re not reaching out to complain. They’re bouncing and buying from someone else.
Getting your navigation and filters right isn’t just about user experience (although that’s a big deal). It’s one of the most important things you can do for your eCommerce SEO. Your nav creates the internal link structure that helps Google — and AI tools like ChatGPT and Perplexity — understand what your store sells and how it’s organized. When your site architecture is clean, search engines can crawl it better, index it faster, and rank it higher.
So whether you just launched your Shopify store or you’ve been at this for years and possibly skipped a few steps along the way… let’s get this right.
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Why Your Navigation Menu Matters for Sales and SEO
Think of your navigation menu and collection filters as the sales associate in a brick-and-mortar store.
Anyone who’s shopped in real life knows not all sales associates are created equal, right?
A bad one stays silent, avoids eye contact, and gives you vague directions. You end up wandering around, getting frustrated, and leaving without buying anything.
A good one greets you, asks a few questions to figure out what you’re looking for, and then walks you directly to the right spot — or at minimum gives you clear directions to get there.
Your navigation menu and collection filters are doing one of those two things right now. They’re either helping people find what they need, or they’re creating friction. And when it’s friction, customers don’t file a complaint. They just leave.
We want yours to be the good associate.
Navigation Menu vs. Collection Filters: What Goes Where?
In most cases, your navigation and filters will have a lot of overlap. If you’d create a collection for something, it should also be a filter. The navigation is for browsing top-down. Filters are for narrowing down once someone is inside a collection.
This is one of the things I see store owners get hung up on the most. And the truth is, there are multiple paths people take when shopping your site. Some go straight to the nav and dig into subcollections. Others go to a parent category and use filters to narrow down. Some skip all of that and go straight to the search bar.
Our goal is to serve all of them, regardless of the path they take. That’s why you’ll have repetition between your navigation and filters… and that’s by design.
Let me give you a couple of examples to show what I mean.
Jewelry store example
If you sell jewelry in both gold and silver, it makes sense to have a subcollection for each metal AND a filter for each. A shopper could go into the gold jewelry collection and filter by product type (necklace, earring, ring). Or they could go into the necklace category and filter by metal (silver or gold). Both paths get them where they need to go.
Apparel example
You definitely want a color filter so shoppers can narrow down results. But would you create a separate subcollection for every color of clothing you sell? Probably not. Unless you’re White House Black Market — do they still exist? — and color IS your entire thing.
There are always nuances depending on what you sell and your specific product assortment. But a good rule of thumb: if I would make a collection for this, it should also be a filter. That rule doesn’t apply perfectly in reverse, but it’ll get you about 90% of the way there.
How to Organize Your eCommerce Navigation Menu
Organizing your navigation comes down to two questions: How does someone shop for what you sell? And what’s most important to your business?
Let’s start at the top.
What Should Go in Your Top-Level Navigation
How you set up your top-level nav depends on the size of your product assortment.
If you have a one-product or one-category store, you don’t need much up there. Your shop link, a quiz or product guide if you have one, and that’s about it. For a store like this, information links like About and Contact can live in the top nav without causing clutter.
If you have a wider product assortment, your top-level items should be the main parent categories of what you sell. For a jewelry store, that’s Necklaces, Earrings, Rings, Bracelets. For apparel, it might be Tops, Bottoms, Dresses.
Once your nav is doing that much heavy lifting, information links, About, Contact, Affiliates, move to the footer. They don’t need prime real estate when your customer is there to shop.
The one exception: wholesale. If wholesale is a real revenue driver for your business, it can stay in the header. If it’s a side thing, footer only.
This is also where your New Arrivals and Best Sellers collections live, if those are relevant to your store.
What About Products That Don’t Fit Neat Categories?
Not every store falls into clean product-type categories, and that’s okay.
I worked with a client who sells handmade keepsakes and gifts for kids, milestone cards, personalized baby blankets, bookends, art display boards, memory books. Very different product types that don’t obviously group together.
Instead of organizing by product type, we created use-case categories. We landed on Milestones, Kids Decor, and Keepsakes & Gifts. Milestone cards and baby blankets went under Milestones. Bookends and art display boards under Kids Decor. Memory books under Keepsakes & Gifts.
When product type doesn’t give you a clean answer, think about what the customer is actually trying to do or celebrate — and organize around that intent.
How to Set Up Subcollections That Actually Help Shoppers
Once your top-level categories are sorted, the next question is what lives underneath them.
Same two questions apply: How does your customer shop? And what’s driving your business?
For some stores, subcollections are straightforward. If you sell apparel by gender at the top level, then under Women’s you’ve got Tops, Bottoms, Dresses. Clean and logical.
But then you layer in the business strategy piece. When I had my brick-and-mortar boutique, denim was a huge revenue driver. Even though denim technically lives under Bottoms, I pulled it into its own top-level category, because denim shoppers are looking for denim, not browsing through Bottoms hoping to stumble across it.
Think about what that category is for your store. It might deserve more visibility than a logical product hierarchy would give it.
For stores with more complex assortments, your subcollections might not even be shoppable collections. Sometimes they’re just organizational headings that group things visually in the menu.
I worked with a skincare client who has her own spa and an online store. Under her top-level Skincare category, her second-level items are things like Category, Specialty, and grouped skin concerns like Appearance, Acne, and Texture. Those aren’t collections people shop directly, they’re a way to organize what’s underneath so the menu doesn’t become a wall of links.
And one more thing to ask yourself about subcollections: do you actually have enough products to justify it? A subcollection with two or three products isn’t helping anyone — it’s just friction. If you don’t have enough inventory to fill it out, keep those products in the parent category and let your filters do the work.
Should You Put Named Collections in Your Navigation?
Named collections, like “The Wanderer Collection” or “Summer Solstice Edit,”are great marketing tools. They work really well in emails, in ads, on social media.
But they don’t always translate to navigation.
If someone lands on your site for the first time and sees “The Wanderer Collection” in your nav, they have zero idea what’s in there. So if you want to include named collections, make sure you also have descriptive collections alongside them. The new visitor who doesn’t know your brand needs to understand what they’ll find when they click that link.
Same goes for seasonal and holiday collections, feel free to use them during the right time of year. Just make sure you remember to remove them when the season’s over.
How to Plan Your Navigation Menu Step by Step
Your navigation is highly dependent on your product assortment. The right nav for one clothing boutique will look different from another.
Here’s what I’d recommend:
- Grab a spreadsheet and start listing out every possible collection. Don’t worry about organization yet — just get it all out of your head.
- Go back through and start grouping, refining, and removing. Ask yourself: would someone shop this way? Does this collection have enough products?
- Map out your hierarchy — what’s top-level, what’s a subcollection, what’s just a filter.
- Test it. Click through your nav like a customer who’s never been to your site before. Does the path make sense?
The good news? It’s not set in stone. You can always adjust it if something isn’t working.
What Collection Filters Should Your Store Have?
You already know the general rule: if you created a collection for it, it should probably be a filter too. But here’s what else to consider.
Product Type or Category Filter
If you sell more than one product type, this is a must. If you’re on Shopify, product type is a default filter option and easy to set up. Just make sure you’re filling in the Product Type field accurately in your Shopify admin. That field powers the filter — if it’s blank or inconsistent, the filter won’t work properly.
Price Filter
If you carry the same type of product across a wide range of price points, a price filter matters. Think about a retailer like Amazon — search for black stilettos and you’ll see styles from $30 to $1,000. At my previous day job, we had similar products ranging from $30 to $200. In cases like that, customers need a way to narrow by budget.
If all your products are around the same price, or you only have one version of each product type? Skip it. It’s not adding value.
Color, Scent, or Flavor Filter
This one seems obvious, but there are a few things to keep in mind.
Group where it makes sense. If you re-sell products from popular brands that have unique scent names, you want to keep the brand name (like “Sweet Strawberry”) so the customer recognizes it. But in your filters, combine them all under “Strawberry.”
Think about quantity. If you have one strawberry item, one raspberry item, and one orange item… instead of individual filters for each flavor, just group them under “Fruit.”
Same goes for prints. If you have a couple leopard items, a zebra, and a snake — group them under “Animal Print” rather than listing each one individually.
Style Filter
Style filters make sense in two situations.
First, if you broke something out into a subcollection (like maxi dresses), you definitely want that as a filter too so people can find it from multiple paths.
Second, sometimes a style filter is necessary even when you didn’t create a collection for it. I worked with a client who sells embroidery kits. She has a lot of different SKUs, so in her filters we grouped the design styles under categories like Flora, Fauna, and Winged Creatures. It didn’t make sense to create separate collections for these — the core product is embroidery kits — but the style filters were incredibly helpful for shoppers browsing inside the collection.
Be Clear Over Clever with Your Link Names
This is worth its own callout because it matters for both your customers and your SEO.
When naming your navigation links, subcollections, and filters, always go with descriptive, obvious names. “Necklaces” beats “Neck Candy.” “New Arrivals” beats “Just Dropped.”
Your first-time visitor needs to know exactly what they’re going to find when they click. And search engines need those descriptive keywords in your navigation links to understand what each page is about. Clear link names create keyword-rich internal links across your entire site, which is one of the simplest things you can do for eCommerce SEO.
Additional Resources
- Badass Basics Episode #1: Your eCommerce Home Page
- Shopify Secrets
- The Lounge Membership: Includes access to SEO Badassery
Frequently Asked Questions
How many items should be in my top-level navigation?
It depends on your product assortment. Single-product stores might only need a Shop link and a product guide. Stores with a wider range should stick to their main product categories as top-level items. The key is keeping it scannable — if your customer has to read through 15 top-level links to find what they need, you’ve got too many.
Should my navigation and filters have the same options?
Mostly, yes. If you created a collection for something, make it a filter too. The reverse doesn’t always apply — some attributes like color or price range work great as filters but don’t need their own collection. The overlap between nav and filters is intentional because different shoppers use different paths.
When should I remove a subcollection from my navigation?
If a subcollection only has two or three products, it’s creating friction, not helping. Keep those products in the parent collection and let your filters handle the rest. You can always add the subcollection back when you have enough inventory to justify it.
Should named collections go in my navigation menu?
Only if you also include descriptive collections alongside them. A returning customer might know exactly what a named collection like “The Wanderer Collection” is, but a first-time visitor won’t. Always make sure new shoppers can find what they need using clear, descriptive category names.
How do I organize navigation when my products don’t fit into standard categories?
Think about how your customer shops, not just what the product technically is. Use-case categories or occasion-based groupings can work really well. If your customer is shopping for a baby shower gift, organizing by Milestones or Keepsakes & Gifts makes more sense than separating out every product type.
Does my navigation menu affect my SEO?
Yes — significantly. Your navigation creates internal links across your entire site, which helps search engines understand your site structure and pass authority to your most important pages. Using clear, descriptive text in your nav links gives search engines keyword context for each page. A well-structured navigation also helps AI search tools understand what your store sells and how your products relate to each other, which affects whether your site gets cited in AI-generated answers.
How often should I update my navigation menu?
Revisit it whenever your product assortment changes significantly — new categories added, old ones discontinued, seasonal shifts. Do a full audit at least once or twice a year to make sure your nav still reflects how customers actually shop and what’s driving your business. Always remove seasonal or holiday collections when they’re no longer relevant.
