Whilst you could use the scheme, there’s no real benefit to use the cycle to work scheme through your limited company. The scheme is there for employees to save tax by essentially buying it from their employer, who reclaims the VAT, through salary sacrifice.
Since your salary should already be set low to reduce your tax liability, a salary sacrifice would not benefit you. That said, there are other options open to you. Your company could buy the bike outright and 'lend' it to you if the certain HMRC rules apply.
If you lend or hire a bicycle or cycling safety equipment to an employee, there are no reporting, tax, or NICs requirements if the following conditions are met:
the bicycles or equipment are available to all your employees
the bicycles or equipment are used mainly for "qualifying journeys" as described below.
A journey only counts as a qualifying journey in two situations:
if all or part of the journey is between home and workplace
if all or part of the journey is between workplaces.
This will give the same corporation tax saving, and you’d also be able to reclaim the VAT (unless using the flat rate scheme).
The other option would be to purchase the bike personally and claim back business mileage at 20p per mile.
If you use the bike under company ownership, record the purchase of the bicycle as ‘Fixed Assets > Equipment Cost’:
Record the costs of running the bicycle as ‘Motor Expenses > Company Bicycle Running Costs’:
If you own the bike personally, see here for how to calculate the mileage, and then record the expense in Crunch using the category ‘Motor Expenses > Mileage Allowance’: