Will yellow bonsai leaves turn green again?

Usually not. A leaf that has lost its chlorophyll rarely recovers it, and that is fine. Judge whether the tree is recovering by whether the next flush of growth comes in a healthy green, not by watching the yellow leaves.

Should I pull the yellow leaves off?

Only if they are already loose or fully dead. Removing them makes no difference to the tree's health, and a leaf still partly green is still feeding the tree. Removing dead material does help air move through a dense canopy.

My bonsai has yellow leaves and the soil is wet. Should I water it?

No. Wet soil with limp yellow foliage is the signature of overwatering, and the tree looks thirsty precisely because its roots can no longer work. Let the soil approach dryness and check the roots if it does not improve.

Is it normal for a few leaves to go yellow?

Yes. Trees shed their oldest leaves continuously, and a handful of yellow leaves low down on an otherwise vigorous tree is ordinary turnover. What is not normal is yellowing that starts on new growth or spreads quickly.

My tree is yellow all over in autumn. Is something wrong?

Almost certainly not, if it is deciduous. Autumn colour and leaf fall are the normal seasonal cycle for species such as maples, elms and larches, and the tree will leaf out again in spring.

Bonsai Leaves Turning Yellow

Yellow leaves on a bonsai almost always mean the roots are in trouble, not the leaves.

The short answer

Yellow leaves on a bonsai almost always mean the roots are in trouble, not the leaves. Feel the soil first: wet and heavy points to overwatering or root rot, dry and light to underwatering. If the moisture is normal, look at whether the yellowing is uniform (usually light or feeding) or between the veins (usually a nutrient problem), and turn a leaf over to rule out pests. Old leaves at the base yellowing a few at a time is normal and needs nothing done.

Work out which one it is

Feel the soil two centimetres down and lift the pot. Wet, heavy soil with limp yellow leaves means overwatering, and root rot if it has been going on for weeks. Bone dry and unusually light means underwatering. Normal moisture sends you to the next check.
Look at the pattern on a yellow leaf. Yellow between the veins while the veins stay green is classic nutrient deficiency. A uniform pale wash across new growth, with long weak stems reaching for the window, is insufficient light. Scorched brown edges with a yellow halo, on a tree fed recently, is fertilizer burn.
Turn two or three leaves over and check the undersides and the leaf axils. Fine webbing and a dusty stippled look is spider mites. Clusters of soft green or black insects on new shoots is aphids. Hard limpet-like bumps that do not brush off is scale. Sticky leaves or a black sooty film means one of those three has been feeding for a while.
Ask where on the tree the yellow leaves are, and how many. A few of the oldest leaves at the base of the tree, shed gradually, is normal ageing and needs no action. Yellowing that starts on new growth, or spreads across the whole canopy in days, is not.

What it is likely to be

Condition	Pick this one when
Overwatering	Soil is still wet days after watering, foliage is limp, growth is slow. The most common answer by a wide margin.
Root Rot	Wet soil plus a sour smell, and roots that are brown, black or mushy rather than firm and pale. This is the version of overwatering that kills.
Underwatering	Soil is dry and the pot is light. Leaves are crisp rather than limp, often browning at the edges first.
Nutrient Deficiency	Soil moisture is normal, roots are healthy, and the yellow sits between green veins. Common in trees not fed for a season or in exhausted soil.
Insufficient Light	Pale washed-out colour with stretched, leggy growth reaching towards the light. Typical of an indoor tree over winter.
Over-fertilizing	Yellowing with scorched brown leaf margins, shortly after feeding, or a white crust on the soil surface.
Spider Mites	Fine stippling that reads as yellow speckling at arm's length, with webbing in the leaf axils. Worst in hot dry indoor air.
Aphids	Yellowing and distortion on the newest shoots, with visible clusters of insects and sticky residue.
Scale Insects	General yellowing and decline with hard brown bumps along the stems and undersides of leaves.
Repot Shock	The tree was repotted or root-pruned in the last few weeks. Yellowing and leaf drop follow root disturbance and usually pass.
Verticillium Wilt	Yellowing and wilting confined to one branch or one side of the tree while the rest looks well. Uncommon, and serious.

Common questions

Will yellow bonsai leaves turn green again?: Usually not. A leaf that has lost its chlorophyll rarely recovers it, and that is fine. Judge whether the tree is recovering by whether the next flush of growth comes in a healthy green, not by watching the yellow leaves.
Should I pull the yellow leaves off?: Only if they are already loose or fully dead. Removing them makes no difference to the tree's health, and a leaf still partly green is still feeding the tree. Removing dead material does help air move through a dense canopy.
My bonsai has yellow leaves and the soil is wet. Should I water it?: No. Wet soil with limp yellow foliage is the signature of overwatering, and the tree looks thirsty precisely because its roots can no longer work. Let the soil approach dryness and check the roots if it does not improve.
Is it normal for a few leaves to go yellow?: Yes. Trees shed their oldest leaves continuously, and a handful of yellow leaves low down on an otherwise vigorous tree is ordinary turnover. What is not normal is yellowing that starts on new growth or spreads quickly.
My tree is yellow all over in autumn. Is something wrong?: Almost certainly not, if it is deciduous. Autumn colour and leaf fall are the normal seasonal cycle for species such as maples, elms and larches, and the tree will leaf out again in spring.

Bonsai Leaves Turning Yellow at a glance

Also known as	Yellowing leaves, chlorosis, leaves going yellow
Affected parts	Leaves first; the cause is usually at the roots
Most at risk	All species. Indoor trees in winter and any tree in dense, water-retentive soil
Main cause	Most often overwatering, which suffocates the roots so the tree cannot take up water or nutrients
Severity	Depends entirely on the cause. Harmless if it is autumn colour or old leaves; fatal within weeks if it is root rot
Reversible?	Usually yes once the cause is corrected. Leaves already yellow rarely turn green again; judge recovery by the next flush

What to look for

Leaves: Loss of green ranging from a pale even wash to bright yellow. Note whether it is uniform, between the veins, or speckled, and whether it started on old leaves or new ones.
Soil: Moisture is the deciding evidence. Also look for algae or a sour smell, which point to constant wetness, and for a white salt crust, which points to over-feeding.
Roots: Firm and pale is healthy. Brown, soft or foul-smelling roots mean root rot and change the answer completely.
Whole tree: Weak, slow growth and gradual leaf loss across the canopy suggest a root or light problem. Yellowing confined to one branch suggests damage or disease in that branch.

Overview

Yellowing is a symptom, not a diagnosis. A leaf turns yellow when chlorophyll breaks down faster than the tree replaces it, and that happens for a dozen different reasons, from a perfectly healthy tree shedding an old leaf to roots that have already rotted away. Thirteen of the conditions covered on this site list yellow leaves among their signs, so the useful question is never "why are my leaves yellow" but "which of these is it", and that is settled by three quick checks rather than by staring at the leaf.

The single most likely answer is overwatering. It is also the most counter-intuitive one, because an overwatered tree looks thirsty: waterlogged soil holds no air, the roots suffocate and stop working, and a tree that cannot draw water up wilts and yellows exactly as a dry one does. Reaching for the watering can at that point is what kills it.

Causes

In rough order of how often it is the answer on a bonsai: soil kept too wet, roots already rotting, soil allowed to dry out completely, no feeding for a season or more, too little light, too much fertiliser, sap-sucking pests, recent root disturbance, and finally the ordinary shedding of old leaves that every tree does.

Commonly confused with

Autumn colour and normal leaf turnover are mistaken for illness every year. A deciduous tree yellowing across the whole canopy in October is doing what it is supposed to do. A tree shedding two or three of its oldest, lowest leaves at any time of year is also normal. Treat those and you will do harm rather than good.

Which species are affected

Every species. Which cause is most likely shifts by species: dry-loving trees such as junipers, pines and jades yellow from overwatering far more often than from anything else, while thirsty broadleaves such as elms and maples are the ones most often found dry.

Treatment

Do not treat the yellowing. Treat whatever the checks above identified, on that condition's own page. The one thing worth doing immediately in every case is to stop watering until you have felt the soil, because the most likely cause is already too much water and the instinct on seeing a sad tree is to give it more.

Prevention

Water by checking the soil rather than by the calendar, in a gritty free-draining mix, in a pot sized to the tree. Feed through the growing season. Give the tree as much light as its species wants. Check the undersides of leaves whenever you water, which takes seconds and catches pests while they are still treatable.