Fire exclusion and past management have altered the composition, structure, and function of frequent-fire forests throughout western North America. In mixed-conifer forests of the California Sierra Nevada, fire exclusion has exacerbated the effects of drought and endemic bark beetles, resulting in extensive mortality of fire-adapted pine species. Thinning and prescribed fire are widely used in these forests to reduce fuels, moderate fire behavior, and restore ecosystems. Tree regeneration influences future forest composition and structure, and therefore future resilience to disturbances, but long-term effects of thinning and prescribed burning on tree regeneration after prolonged fire exclusion are poorly understood. We measured tree regeneration one year prior to, and periodically for 16 years following thinning and prescribed burning in a mixed-conifer forest in the Sierra Nevada, California, USA. We asked three questions. How did the composition and density of tree regeneration change after thinning and prescribed burning? Did pretreatment vegetation types influence conifer regeneration density after treatments? Did planting after overstory thinning increase regeneration density of native pine species?Sixteen years after treatments, combined natural regeneration of shade-tolerant white fir (Abies concolor) and incense-cedar (Calocedrus decurrens) averaged 2,032 trees per hectare (tph) after understory thinning, and 7,745 tph after understory thinning combined with prescribed burning, increases of 37 % and 146 % from pretreatment densities. In contrast, combined natural regeneration of white fir and incense-cedar averaged 497 tph after overstory thinning, 780 tph after overstory thinning with prescribed burning, 113 tph after prescribed burning alone, and 807 tph in untreated controls, all of which were declines from pretreatment densities. Natural regeneration of white fir and incense-cedar was consistently an order of magnitude greater than Jeffrey pine (Pinus jeffreyi) and sugar pine (Pinus lambertiana), whose combined densities 16 years after treatments averaged 37 tph across treatments and did not significantly respond to thinning and/or prescribed burning. Natural conifer regeneration after treatments varied by pre-treatment vegetation type (closed canopy, Ceanothus cordulatus shrub dominated, and open sparse), with large increases of natural regeneration after understory thinning in closed canopy and Ceanothus shrub vegetation types. Planting increased sugar pine regeneration density after overstory thinning, marginally increased Jeffrey pine regeneration after overstory thinning combined with prescribed burning, and increased white fir regeneration after overstory thinning with and without burning. No treatments reduced white fir and incense-cedar natural regeneration while simultaneously increasing natural pine regeneration, suggesting new thinning, burning, and planting approaches may be required to meet regeneration restoration objectives.