More than 90% of the commercial egg production in the United States is pledged to be in cage-free systems by 2025. Management practices like induced molting and litter area management have come under scrutiny because of the housing system change. The aim of this study was to determine the welfare and production implications of different litter substrates and also evaluate induced molting of hens in a cage-free system. Bovan White hens were housed in a multi-tier aviary system with daily access to open litter area of either Astroturf (AT), wood shavings (SH), or straw (ST) and bare concrete floor (CO) serving as control. At 68 wk of age, molt was induced in half of the hens whereas the other half continued without molting to 116 wk. Production and welfare parameters were measured periodically throughout first and second cycles. Litter substrate did not influence hen-day production and case-weight measurements. However, CO had the lowest total number of eggs produced during the first cycle (P < 0.05). Hen-day percentage was approximately 14% greater in molted hens during the second cycle with egg case weight being heavier in non-molt hens toward the end of second cycle (P < 0.05). The only welfare parameter influenced by litter substrate during the first cycle was a greater crop feather loss in AT than ST at mid-lay (P < 0.05). Keel deformations increased with age irrespective of the litter substrate with 91.5% of palpated hens having keel deformations at the end of first cycle (P < 0.05). Molting did not influence the keel palpation and footpad scores whereas frequency of moderate comb wound was greater in molt hens during molt (P < 0.05). Severe feather loss was seen in non-molt hens during the second cycle (P < 0.05). Litter substrate does not affect production and physical parameters of welfare of hens in a multi-tier aviary system. Additionally, induced molting can be successfully carried out in the multi-tier cage-free system.