How to Start Seeds Indoors: A Step-by-Step Guide

Every crop guide on this site assumes you can get a seed to come up and survive its first two weeks. That step gets skipped over constantly, and it’s where most indoor gardens actually end — not at the “my basil turned yellow” stage, but earlier, at “nothing came up” or “it came up pale and fell over.”

This article contains no affiliate links, which is why there’s no disclosure box above. It’s the general method: how to read a seed packet, what depth and warmth different crops want, and how to get a seedling from the soil surface to a light source before it stretches itself thin trying to find one.

Why almost everything here starts from seed

Garden centers sell “starts” — young plants already a few weeks old — bred and hardened for a spot in a garden bed. Indoors, that shortcut mostly doesn’t exist. Herbs and greens compact enough for a windowsill are rarely sold as starts, and the ones that are have usually spent their whole short life in a heated greenhouse, not a house. You sow seed, almost every time.

That’s not a downside. Seed is inexpensive enough that a $3 packet of basil outlasts a $6 supermarket pot that’s already past its best, and starting from seed is the only way to grow the dwarf and cut-and-come-again varieties bred specifically for containers rather than garden rows.

The three things that decide whether seeds come up

Reading a seed packet in 30 seconds

Every seed packet answers the same four questions, usually in a single line of small print near the bottom:

• Sowing depth — how deep to bury it.
• Days to germination — how long before you should expect to see green.
• Spacing — how far apart, which matters more once you thin.
• Days to maturity — counted from sowing for most crops, but from transplant for a few (tomatoes and peppers are the common exception — check the packet).

If the packet says nothing about depth, the general rule is to bury a seed roughly twice as deep as it is wide. Dust-fine seed (lettuce, most herbs) gets barely covered or not covered at all; a seed the size of a peppercorn (radish, peas) goes under a proper half inch.

What you need before you sow

• A container with drainage holes — a purpose-made seed tray, or a reused yogurt pot or takeaway container with holes poked in the bottom.
• Seed-starting mix, not garden soil and, ideally, not a heavy all-purpose potting mix either. It’s lighter, finer and sterile, which matters most for small seed sown in cells (see below).
• A clear lid or a sheet of cling film to hold humidity until germination.
• A spray bottle or a watering can with a fine rose, so you’re misting rather than flooding a shallow tray.
• Labels. Two trays of unlabelled seedlings look identical, and you will not remember which is which by day ten.
• Your light source already set up and switched on, not something you’ll sort out once seeds germinate. By the time green shows, it’s already late to start looking for a light.

Seed-starting mix, potting mix, or garden soil?

Garden soil is out regardless of what you’re sowing — it compacts hard in a small container, drains poorly, and can carry outdoor pests and weed seed indoors.

Between the other two, it depends on the seed. A large seed sown directly into its final pot — a dwarf tomato, a radish, a pea — germinates fine in an ordinary potting mix, because it’s carrying enough of its own energy reserve to push through. A fine seed sown thickly in a shallow tray — lettuce, basil, most microgreens — does better in a proper seed-starting mix: it holds even moisture without waterlogging, and its sterility cuts down on the fungal issues that take out a tray of tiny, crowded seedlings before you’d notice anything else was wrong.

If you’re only ever going to buy one bag, buy the seed-starting mix and use it for both. The reverse doesn’t work as well — a coarse potting mix is a poor bed for seed that’s smaller than a pinhead.

Step by step: sowing indoors

1. Fill the container with pre-moistened mix — damp like a wrung-out sponge, not dry and not dripping — and level the surface without packing it down hard.
2. Sow at the packet’s stated depth and spacing. For dust-fine seed, scatter it across the surface and press it in gently with your palm rather than burying it.
3. Cover, if the seed needs darkness to germinate (most does) — a light sprinkling of mix or vermiculite for larger seed, nothing at all for the dust-fine kind if the packet says it needs light.
4. Mist the surface rather than pouring, which can wash small seed sideways or bury it too deep.
5. Cover with the lid or cling film and set it somewhere warm. A spot that stays around 70°F (21°C) works for most crops; check the table below for the exceptions.
6. Check daily. Mist if the surface has started to dry. Remove the cover the moment the first seedlings appear — trapped humidity that helped germination becomes a fungal risk once there’s a plant to rot.

Depth, temperature and germination time by crop

Crop	Sowing depth	Best germination temp	Days to germinate	Needs darkness?
Microgreens (radish, mustard)	Surface, uncovered	65–75°F (18–24°C)	2–4	✓Yes
Lettuce (loose-leaf)	Surface or a 5mm cover	65–75°F (18–24°C)	5–10	–No
Basil	6mm (¼ in)	70–75°F (21–24°C)	5–10	✓Yes
Radish	12mm (½ in)	65–75°F (18–24°C)	3–5	✓Yes
Spinach	12mm (½ in)	60–65°F (15–18°C)	7–14	✓Yes
Parsley	6mm (¼ in)	65–70°F (18–21°C)	14–28	✓Yes
Dwarf tomatoes	6mm (¼ in)	75–80°F (24–27°C)	5–10	✓Yes

General horticultural guidelines, not measurements from a specific sowing — actual timing varies with seed freshness, moisture and your own conditions. Spinach is the one crop here where warmth actively hurts germination rather than helping it. See each crop's full guide, linked below the table, for the complete method.

For the crops that have a full guide on this site: basil, spinach (spinach’s cool-germinating habit is unusual enough that it gets its own troubleshooting section), and dwarf tomatoes, where sowing is only the first four to six weeks of a longer timeline to transplant. Microgreens have their own quick method, including the blackout period that isn’t needed for anything else on this list, in microgreens in ten days.

The first two weeks after germination

The moment you see green, light becomes urgent — not optional, not tomorrow. A seedling under weak or absent light stretches toward whatever brightness it can find: the stem thins, elongates, and leans. This is called legginess, it happens within days, and it doesn’t reverse. Move the tray under real light — a bright window or a grow light — the day the first seedling shows.

Thin crowded seedlings once true leaves appear. The first pair of leaves a seedling produces are seed leaves (cotyledons), not the plant’s actual leaf shape — wait for the second set, the “true leaves,” before judging which seedlings to keep. Snip the weakest at soil level with scissors rather than pulling, which disturbs the roots of whatever’s growing next to it.

Water from below where you can. Pour a little water into an outer tray and let the mix draw it up, rather than watering overhead into a dense planting — it’s the same principle used for microgreens, and it keeps water off young stems, which is where damping off gets its start.

Start feeding once the second set of true leaves is out, not before. Seed-starting mix carries little to no nutrition by design, but a seedling runs on its own seed reserves for the first week or two regardless. A liquid feed at quarter strength is enough at this stage — see the full fertilizing guide for when and how much to step that up as plants establish.

Direct sow, or start in cells and transplant?

Both work indoors; the right choice depends on the crop and how much you’re growing.

Sow direct, into the final pot, for anything that dislikes root disturbance or that you’re growing at high density — lettuce, spinach, radish, microgreens, most greens grown for cut-and-come-again harvest. One less step, one less shock to the plant.

Start in small cells and transplant later for anything you’re starting weeks ahead of when it’ll actually live in its final spot, or anything where you want to select the strongest few seedlings from a larger batch — dwarf tomatoes are the clearest example on this site, typically sown four to six weeks before they move to their final container.

Neither method works for a plant better propagated from a cutting than a seed in the first place — mint is the obvious exception among common indoor herbs, and rooting it from a cutting is both faster and more reliable than starting it from seed. Scallions are an even shorter cut: regrow the white root ends from a bunch you already bought, with no seed involved at all — along with a few other kitchen scraps that regrow reliably, and several that don’t despite the internet’s claims.

Common mistakes

Buying seed-starting mix and then burying seed exactly as deep as the packet’s outdoor spacing chart suggests. Outdoor charts often assume direct sowing into a garden bed with more margin for error. Indoors, in a shallow tray, err toward the shallow end of any depth range.

Leaving the humidity dome on after germination. It did its job getting the seed to sprout; left on afterward it’s just an incubator for the fungus that causes damping off.

Sowing everything at once, at full density. A packet contains far more seed than one windowsill needs. Sow a fraction, keep the rest cool and dry in its original packet, and most vegetable and herb seed stays viable for two to three years.

Assuming nothing coming up means bad seed. Temperature is the far more common culprit — too cold for most crops, too warm for the handful (spinach chief among them) that prefer it cool. Check the table above before assuming you need new seed.

Frequently asked questions

Do all seeds need to be covered with soil? No. Some, mostly fine seed like lettuce and many herbs, germinate better with light exposure and want to sit on the surface or under only a dusting of mix. Others need complete darkness. The table above lists the common ones; when in doubt, the seed packet says which.

Do I need a heat mat? Not for most greens and herbs — normal room temperature covers the 65–75°F range they want. It’s more useful for warmth-loving crops like tomatoes and peppers, which germinate faster and more evenly with the soil a few degrees warmer than the room — peppers in particular want it closer to 80–85°F.

How long does seed actually last in storage? Most vegetable and herb seed stays viable for two to three years if kept cool and dry, with germination rates declining gradually rather than seed becoming useless overnight. Onion and parsnip seed are shorter-lived exceptions, good for closer to a single year.

Can I start seeds in an old yogurt pot? Yes — poke drainage holes in the bottom and it works as well as a purpose-bought tray. The container matters far less than depth, warmth and not letting it dry out.

My seedlings came up but immediately flopped over. What happened? Almost certainly damping off — see the callout above. It’s a moisture and ventilation problem, not a light or seed problem, and there’s no fixing an affected seedling once it collapses.

Where to go next

This is the method; the beginner setup checklist covers the decisions that come before it — which crops to pick and how to audit your light — and what comes after, once seedlings are established. If you already know which crop you’re starting, its full guide covers the rest of the growing cycle from here: basil, spinach, or dwarf tomatoes.