If filing as Married Filing Separate and both spouses have pension income and meet the eligibility requirements, the exclusion of up to $12,000 is prorated between them in the ratio that each spouse's pension relates to the total pension received by both spouses.
If only one spouse has pension income and meets the eligibility requirements, that spouse takes the entire exclusion of up to $12,000. The spouse who has no pension income receives no exclusion.
For additional information about Iowa Pension/Retirement Income Exclusion go here.