Determining best practices for managing free farrowing systems is crucial for uptake. Cross-fostering, the exchange of piglets between litters, is routinely performed amongst crate-housed sows. However, cross-fostering can increase fighting amongst the litter and may be more challenging within free farrowing systems as sows have more freedom to respond to cross-fostered piglets. This study compared the effect of either cross-fostering (FOS), or a control of sham-fostering (CON), of four focal piglets per litter on Day 6 postpartum in crates (CRATE) and free farrowing pens (PEN). The post-treatment behavioural responses of sows were recorded (Day 6 = 60 min; Day 7 = 300 min; n = 48), as were the average daily gain (ADG; g/day), total weight gain (TWG; kg) and body lesion scores of focal piglets and their littermates throughout lactation (Day 6, Day 8, Day 11 and Day 26; n = 539) and the post-weaning period (Day 29, Day 32 and Day 60; n = 108). On Day 6, though post-reunion latency to nursing did not differ, latency to successful nursing was longer amongst FOS than CON litters (P < 0.001), more so amongst CRATE FOS than PEN FOS (P < 0.01). On Day 7, PEN FOS sows had fewer successful nursing bouts (P < 0.05) and exhibited decreased lateral (P < 0.01) and increased ventral lying frequencies (P < 0.01) compared to all other housing and treatment combinations. Focal piglet ADG was lower for FOS than CON in the CRATE during Day 6 to Day 8 (P < 0.01) and lower in the PEN during Day 6 to Day 8 (P < 0.001), Day 8 to Day 11 (P < 0.01) and Day 11 to Day 26 (P < 0.05). The TWG of pre-weaned focal piglets (Day 6 to Day 26) was higher amongst CON than FOS litters (P = 0.01). Post-weaning, piglet ADG was higher for PEN than CRATE during Day 26 to Day 29 (P < 0.01) and higher for FOS than CON during Day 26 to Day 29 (P < 0.05), Day 29 to Day 32 (P < 0.001) and Day 32 to Day 60 (P < 0.01); thus, TWG was higher for FOS than CON during the weaner (P = 0.001) and the combined lactation and weaner periods (P = 0.09). In conclusion, sow behaviour was disrupted by cross-fostering in the crates and pens and continued to be disturbed on the following day amongst penned sows. FOS piglets exhibited reduced ADG after cross-fostering, which extended throughout lactation in the pens. However, the increased post-weaning weight gain of FOS piglets meant that their TWG was higher than CON piglets, irrespective of the farrowing system used.