Best Trays and Containers for Growing Microgreens: Complete Guide
By Bryan, Microgreens Farmer at Wind River GreensQuick answer: The best trays for growing microgreens are 1-2 inches deep with proper drainage — either built-in holes or a two-tray system — to prevent the mold and root rot that standing water causes. Plastic trays are your most affordable option, while stainless steel lasts longer and sanitizes more easily between cycles. Your container choice directly affects harvest quality, growth speed, and overall success.
Choosing the right trays and containers is crucial for successful microgreen cultivation. The best containers provide proper drainage, adequate growing space, and easy harvesting access while fitting your budget and growing goals.
Whether you're just starting your microgreen journey or scaling up production, the container system you choose will directly impact your harvest quality, growth speed, and overall success rate.
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Understanding Microgreen Container Requirements
Before diving into specific products, it's essential to understand what makes a great microgreen container. Unlike traditional gardening, microgreens have unique needs that require specialized growing setups.
Drainage is absolutely critical. Microgreens need consistent moisture but cannot tolerate standing water, which leads to mold and root rot. The best containers feature either built-in drainage holes or work as part of a two-tray system.
Size matters for root development. Most microgreen varieties need containers that are 1-2 inches deep. Shallow containers work perfectly since microgreens are harvested before developing extensive root systems.
Material choice affects durability and cost. Plastic trays are lightweight and affordable, while stainless steel options offer superior longevity and easier sanitization between growing cycles.
Top Tray Systems for Home Growers
Bootstrap Farmer 10x20 Growing Trays
These heavy-duty plastic trays are incredibly popular among both home growers and small commercial operations. The thick construction prevents cracking and warping, even with regular use.
What makes them special: The extra-strong ridged bottom provides excellent drainage while supporting the growing medium. They're also stackable, making storage simple when not in use.
Best for: Serious home growers who want professional-quality equipment. These trays work beautifully for larger varieties like sunflower and pea shoots that need more space to develop.
Standard 1020 Seed Starting Trays
The classic choice for beginners, these lightweight plastic trays are available at most garden centers. While not as durable as premium options, they're perfect for testing different growing methods.
Drainage considerations: Standard 1020 trays often need additional drainage holes drilled for optimal microgreen growing. Most come with minimal drainage that works fine for traditional seed starting but isn't quite enough for microgreens.
Budget-friendly approach: These trays typically cost under $2 each, making them ideal for experimenting with different varieties before investing in higher-end equipment.
Mesh Bottom Growing Trays
Some growers swear by mesh-bottom containers that allow air circulation from below while providing excellent drainage. These work especially well in greenhouse or controlled environment setups.
Airflow advantages: The mesh bottom promotes healthy root development and reduces the risk of mold issues, particularly important for dense varieties like broccoli and radish microgreens.
Professional-Grade Container Options
Stainless Steel Growing Trays
Restaurant and commercial kitchens often use stainless steel sheet pans that double perfectly as microgreen growing containers. These offer unmatched durability and are incredibly easy to sanitize.
Long-term investment: While more expensive upfront, quality stainless steel trays can last decades with proper care. They're also completely food-safe and won't retain odors or stains.
Size versatility: Available in multiple sizes from quarter-sheet to full-sheet pans, allowing you to match container size to your available space and growing goals.
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Perforated Insert Systems
Many professional growers use perforated inserts that fit inside solid trays, creating a two-level drainage system. This setup provides the ultimate control over moisture levels.
How they work: The perforated top tray holds your growing medium and seeds, while the solid bottom tray catches excess water. This prevents soggy roots while maintaining consistent moisture.
Customization benefits: You can adjust water levels in the bottom tray to fine-tune growing conditions for different microgreen varieties.
DIY Container Solutions
Repurposed Food Containers
Many successful growers start with repurposed takeout containers, yogurt cups, or other food-grade plastic containers. This approach costs almost nothing and works surprisingly well for small-scale growing.
Modification requirements: Most repurposed containers need drainage holes added. Use a heated nail or small drill bit to create 6-8 holes in the bottom.
Size limitations: Smaller containers work best for quick-growing varieties like radish and broccoli microgreens. Larger varieties like sunflower need more root space.
Aluminum Disposable Pans
Disposable aluminum pans from the grocery store make decent temporary growing containers. They're especially useful for testing new varieties or giving away starter kits to friends.
Drainage setup: Poke holes in the bottom with a skewer or knife tip. Space holes about 2 inches apart for optimal drainage.
When to use them: Perfect for one-time growing experiments or teaching children about microgreens. At Wind River Greens, we often recommend this approach for families just getting started.
Container Size Considerations
Matching Container Size to Variety
Different microgreen varieties have varying space requirements that affect container choice. Understanding these needs helps you maximize yields and plant health.
Compact varieties: Radish, broccoli, and mustard microgreens grow well in smaller containers due to their fine root systems and quick growing cycle.
Space-hungry varieties: Sunflower and pea shoots need larger containers to accommodate their more extensive root systems and taller growth habit.
Scaling for Production Goals
Consider your harvesting frequency when choosing container sizes. Larger containers produce bigger harvests but require more seeds, growing medium, and space.
Small batch approach: Multiple smaller containers let you stagger plantings for continuous harvests. This works well for home use where you want fresh microgreens available weekly.
Efficiency considerations: Larger containers reduce the number of individual plantings you need to manage, making them ideal when growing for farmers markets or restaurants.
Drainage Systems Explained
Bottom-Watering vs Top-Watering Setup
Your container choice affects watering methods, which significantly impacts growing success. Understanding these relationships helps you choose the right system.
Bottom-watering benefits: Prevents seed displacement and reduces mold risk by keeping foliage dry. Requires containers that can sit in water trays without becoming waterlogged.
Top-watering considerations: More traditional but requires careful technique to avoid overwatering. Works with any container that has proper drainage holes.
Creating Effective Drainage
Proper drainage prevents the most common microgreen growing problems. Even the best containers need attention to drainage details.
Hole size and spacing: Drainage holes should be large enough to prevent clogging but small enough to retain growing medium. Quarter-inch holes spaced 2-3 inches apart work well for most situations.
Elevation techniques: Raising containers slightly off flat surfaces improves drainage and air circulation. Simple jar lids or cork coasters work perfectly for this purpose.
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Material Comparisons
Plastic vs Metal vs Glass
Each material offers distinct advantages depending on your growing situation, budget, and long-term goals.
Plastic advantages: Lightweight, affordable, and available in many sizes. Modern food-grade plastics are safe and durable enough for years of use.
Metal benefits: Superior durability and heat conduction can actually benefit some growing situations. Stainless steel is completely food-safe and incredibly easy to clean.
Glass considerations: While beautiful and completely inert, glass containers are heavy, breakable, and expensive. Better suited for decorative growing than production.
Food Safety Considerations
Using food-grade containers is essential when growing microgreens for consumption. This becomes especially important if you're considering selling your harvest.
Certification importance: Look for containers marked as food-grade or FDA-approved. Avoid containers that previously held non-food items, even if thoroughly cleaned.
Chemical concerns: Some recycled plastics may contain chemicals that leach into growing mediums. When in doubt, stick with containers specifically designed for food production.
Budget-Friendly Starter Setups
Under $20 Complete Systems
Getting started with microgreen growing doesn't require expensive equipment. Many successful growers begin with simple, affordable container systems.
Basic two-tray system: One solid tray for water collection and one perforated tray for growing. Total cost under $15 for a system that grows enough microgreens for a family.
Repurposed container approach: Free containers from your kitchen plus a $5 bag of growing medium gets you started immediately.
When to Upgrade Equipment
Starting simple makes sense, but knowing when to invest in better containers improves your growing experience and results.
Volume indicators: If you're growing more than 2-3 trays per week consistently, upgrading to professional equipment often pays for itself in improved efficiency.
Quality improvements: Better containers reduce crop losses from drainage problems and make harvesting easier and more pleasant.
Maintenance and Longevity
Cleaning Between Growing Cycles
Proper container maintenance prevents disease buildup and extends equipment life. Different materials require different cleaning approaches.
Plastic container care: Wash with warm soapy water and rinse thoroughly. Occasional disinfecting with diluted bleach solution prevents bacterial buildup.
Metal container maintenance: Stainless steel handles stronger cleaning agents and high temperatures. Dishwasher cleaning works perfectly for most metal containers.
Storage Solutions
When not actively growing, proper storage keeps containers in good condition and ready for use.
Space-saving tips: Stackable containers reduce storage space requirements. Nesting designs work even better for long-term storage.
Organization benefits: Keeping containers clean and organized makes starting new growing cycles faster and more enjoyable.
Matching Your Container to Specific Microgreen Varieties
Not every microgreen variety behaves the same way in the same container, and choosing based on what you're growing can make a noticeable difference in your results.
Dense, heavy crops like sunflower and pea shoots benefit from trays with solid, reinforced bottoms. These varieties produce thick root mats that can actually bow or crack flimsy plastic trays by harvest day, especially if you're growing in warm conditions where root development accelerates. A tray with at least 2mm wall thickness handles the pressure without warping.
Fine-seeded varieties like amaranth, basil, and carrot are better suited to trays with a finer drainage pattern. Large drainage holes can pull small growing medium particles through, creating a mess and drying out unevenly. For these crops, either use a layer of burlap or paper towel over the drainage holes, or choose trays with a ridged bottom and smaller perforations.
Mucilaginous seeds — those that get slimy when wet, including basil, arugula, and flax — do better in trays where airflow across the soil surface is decent. A shallow tray in a well-ventilated spot prevents the moisture from sitting directly against the seed coat too long after germination begins.
Tray Depth by Crop Type
- 1 inch deep: Radish, mustard, broccoli, cabbage, kale — fast growers with shallow roots that don't need extra medium
- 1.5 inches deep: Sunflower, beet, chard — benefit from slightly more medium to anchor their larger seed hulls
- 2 inches deep: Pea shoots, corn shoots — need the extra depth for stable root development and to support the height of the crop at harvest
Growing Medium and How It Interacts with Your Tray
The container and the growing medium work as a system, not independently. A tray that performs well with one medium can underperform with another.
Coco coir drains quickly and stays light, which means it works well in trays with moderate drainage. It dries out faster near the tray edges, so wider trays (like a standard 10x20) may need slightly more frequent bottom watering than narrower ones to keep moisture even across the whole surface.
Soil-based mixes hold more moisture and are heavier. In a thin plastic tray, a soil mix can add enough weight that the tray bows when lifted, particularly once roots have knit through it. If you're using soil, this is another reason to invest in heavier-duty trays with structural support built into the bottom.
Hydroponic growing mats — thin fiber pads used without any loose medium — change the drainage equation entirely. Since there's no loose material to shift or compact, you can use trays with larger drainage holes without worrying about medium loss. These mats work particularly well in shallow trays for quick crops like radish (ready in 7–9 days) where you want to minimize cleanup between cycles.
Sanitizing and Reusing Trays Between Cycles
How easy a tray is to clean should factor into your buying decision, especially if you're running multiple cycles per month.
Plastic trays can be scrubbed and soaked in a diluted hydrogen peroxide solution (3% hydrogen peroxide mixed 1:1 with water works well) for 10–15 minutes to kill off residual mold spores or pathogens. Let them air dry completely before reusing. The limitation with plastic is that scratches from brushes or tools create surface grooves where biofilm can accumulate over time. After 50–100 cycles, even well-maintained plastic trays are worth replacing.
Stainless steel trays tolerate more aggressive cleaning — including food-safe sanitizing sprays and higher-temperature rinses — without degrading. The upfront cost is higher (typically $15–30 per tray versus $1–5 for plastic), but commercial growers running 3–4 cycles per month often find stainless pays for itself within a year through reduced replacement costs alone.
Silicone trays are a less common option worth mentioning. They're flexible, which makes popping out growing medium easier after harvest, and they resist mold well. The drawback is that most silicone options aren't sized to standard 10x20 dimensions, which limits how they fit into existing shelving and humidity dome setups.
Whatever material you use, drying trays fully between cycles is more important than any specific cleaning product. Moisture left sitting in a stacked tray is the most common cause of mold problems in the next round, not inadequate sanitation.
Conclusion
The best trays and containers for growing microgreens balance drainage, durability, and cost while fitting your space and production goals. Whether you choose professional stainless steel systems or start with repurposed containers, proper drainage and food-grade materials are non-negotiable for healthy, safe harvests.
Remember that container choice affects every aspect of your growing experience, from watering frequency to harvest quality. Starting with simple, proven designs lets you learn the basics before investing in specialized equipment that matches your specific needs and growing style.