Weaning pigs into deep-litter (D) housing systems and then moving them into conventional (C) housing facilities affects the growth paths of the pigs and can result in differences in carcass composition which may be explained by altered fat metabolism. To examine this proposition experimentally, 160 female Large White × Landrace pigs were obtained at 3 weeks of age, average liveweight 5.5 ± 0.08 kg and were stratified by weight to four treatments. The treatments consisted of two housing treatments, C or D, across two growth periods: (i) early (3–13 weeks of age); and (ii) late (13–24 weeks of age). At ~13 weeks of age eight pigs per experimental treatment (n = 32) were slaughtered and the remaining pigs (n = 128) moved to new pens where they were housed until slaughter at ~24 weeks of age. To 13 weeks of age, the effect of housing type on lipogenesis did not reach significance (P > 0.05). At 24 weeks of age there were some treatment differences in fatty acid profile (P ≤ 0.05) and the concentration of plasma glycerol (P = 0.002) and non-esterified fatty acids (P = 0.019). There were trends for lipogenic enzyme activity to differ between treatments also (P < 0.100). Results suggested fat deposition was lower in D-finished pigs compared with C-finished pigs, rejecting the hypothesis that D-finished pigs would be fatter. However, most of the differences in the biochemical measurements were explained by the significant reduction in growth that occurred when pigs changed housing environments, rather than as an effect of the housing environment itself. Indicators of lipogenesis suggested that lipogenic rate was lowest in pigs moved from C to D housing compared with other treatment groups that had remained within the same housing, C or D, throughout the experiment or had moved from D housing to C housing at 13 weeks of age.